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Article ; Conference proceedings ; Online: CRYSTALLISATION AND PRELIMINARY CRYSTALLOGRAPHIC STUDIES OF LIPASES

Cleasby, Anne

2024

Abstract: Lipases from two Pseudomonas species have been crystallised in various forms some of which appear suitable for a detailed structural analysis by X-ray crystallography. All crystals were grown using the method of vapour diffusion by hanging drop or ... ...

Abstract	Lipases from two Pseudomonas species have been crystallised in various forms some of which appear suitable for a detailed structural analysis by X-ray crystallography. All crystals were grown using the method of vapour diffusion by hanging drop or sitting drop, at 4C or 15C. Different crystal forms tended to appear at the two temperatures chosen for the crystallisation trials. The two lipases used came from Pseudomonas Amano, and Pseudomonas Glumae. Crystals appeared under different conditions for the two enzymes, but at least one crystal form of each diffracted to greater than 3.0A. The work on P. Amano has as yet gone no further than the ascertation of conditions for crystallisation to occur, but space groups have been determined for three crystal forms of P. Glumae. The first crystals that were tested proved to be trigonal, but were unsuitable for detailed investigation, the two others were both possible candidates for high resolution studies. One form is tetragonal, crystallising in space group P422, the other is orthorhombic, the crystals growing in space group P222, It is on this second form that subsequent structural analysis has been concentrated.
Language	English
Publishing date	2024-03-13
Publisher	GBF Gesellschaft für Biotechnologische Forschung mbH, Braunschweig
Publishing country	de
Document type	Article ; Conference proceedings ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: X-ray Screening of an Electrophilic Fragment Library and Application toward the Development of a Novel ERK 1/2 Covalent Inhibitor.

St Denis, Jeffrey D / Chessari, Gianni / Cleasby, Anne / Cons, Benjamin D / Cowan, Suzanna / Dalton, Samuel E / East, Charlotte / Murray, Christopher W / O'Reilly, Marc / Peakman, Torren / Rapti, Magdalini / Stow, Jessie L

Journal of medicinal chemistry

2022 Volume 65, Issue 18, Page(s) 12319–12333

Abstract: Fragment-based drug discovery (FBDD) has become an established method for the identification of efficient starting points for drug discovery programs. In recent years, electrophilic fragment screening has garnered increased attention from both academia ... ...

Abstract	Fragment-based drug discovery (FBDD) has become an established method for the identification of efficient starting points for drug discovery programs. In recent years, electrophilic fragment screening has garnered increased attention from both academia and industry to identify novel covalent hits for tool compound or drug development against challenging drug targets. Herein, we describe the design and characterization of an acrylamide-focused electrophilic fragment library and screening campaign against extracellular signal-regulated kinase 2 (ERK2) using high-throughput protein crystallography as the primary hit-finding technology. Several fragments were found to have covalently modified the adenosine triphosphate (ATP) binding pocket Cys166 residue. From these hits,
MeSH term(s)	Acrylamides/chemistry ; Adenosine Triphosphate/chemistry ; Crystallography, X-Ray ; Mitogen-Activated Protein Kinase 1/antagonists & inhibitors ; Mitogen-Activated Protein Kinase 1/metabolism ; Protein Kinase Inhibitors/pharmacology ; X-Rays
Chemical Substances	Acrylamides ; Protein Kinase Inhibitors ; Adenosine Triphosphate (8L70Q75FXE) ; Mitogen-Activated Protein Kinase 1 (EC 2.7.11.24)
Language	English
Publishing date	2022-09-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	218133-2
ISSN	1520-4804 ; 0022-2623
ISSN (online)	1520-4804
ISSN	0022-2623
DOI	10.1021/acs.jmedchem.2c01044
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Article ; Online: Crystallographic screening using ultra-low-molecular-weight ligands to guide drug design.

O'Reilly, Marc / Cleasby, Anne / Davies, Thomas G / Hall, Richard J / Ludlow, R Frederick / Murray, Christopher W / Tisi, Dominic / Jhoti, Harren

Drug discovery today

2019 Volume 24, Issue 5, Page(s) 1081–1086

Abstract: We present a novel crystallographic screening methodology (MiniFrags) that employs high-concentration aqueous soaks with a chemically diverse and ultra-low-molecular-weight library (heavy atom count 5-7) to identify ligand-binding hot and warm spots on ... ...

Abstract	We present a novel crystallographic screening methodology (MiniFrags) that employs high-concentration aqueous soaks with a chemically diverse and ultra-low-molecular-weight library (heavy atom count 5-7) to identify ligand-binding hot and warm spots on proteins. We propose that MiniFrag screening represents a highly effective method for guiding optimisation of fragment-derived lead compounds or chemical tools and that the high screening hit rates reflect enhanced sampling of chemical space.
MeSH term(s)	Crystallography ; Drug Design ; Ligands ; Molecular Weight ; Small Molecule Libraries
Chemical Substances	Ligands ; Small Molecule Libraries
Language	English
Publishing date	2019-03-14
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	1324988-5
ISSN	1878-5832 ; 1359-6446
ISSN (online)	1878-5832
ISSN	1359-6446
DOI	10.1016/j.drudis.2019.03.009
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Article: Fragment-based screening using X-ray crystallography and NMR spectroscopy.

Jhoti, Harren / Cleasby, Anne / Verdonk, Marcel / Williams, Glyn

Current opinion in chemical biology

2007 Volume 11, Issue 5, Page(s) 485–493

Abstract: Approaches which start from a study of the interaction of very simple molecules (fragments) with the protein target are proving to be valuable additions to drug design. Fragment-based screening allows the complementarity between a protein active site and ...

Abstract	Approaches which start from a study of the interaction of very simple molecules (fragments) with the protein target are proving to be valuable additions to drug design. Fragment-based screening allows the complementarity between a protein active site and drug-like molecules to be rapidly and effectively explored, using structural methods. Recent improvements in the intensities of laboratory X-ray sources permits the collection of greater amounts of high-quality diffraction data and have been matched by developments in automation, crystallisation and data analysis. Developments in NMR screening, including the use of cryogenically cooled NMR probes and (19)F-containing reporter molecules have expanded the scope of this technique, while increasing the availability of binding site and quantitative affinity data for the fragments. Application of these methods has led to a greater knowledge of the chemical variety, structural features and energetics of protein-fragment interactions. While fragment-based screening has already been shown to reduce the timescales of the drug discovery process, a more detailed characterisation of fragment screening hits can reveal unexpected similarities between fragment chemotypes and protein active sites leading to improved understanding of the pharmacophores and the re-use of this information against other protein targets.
MeSH term(s)	Binding Sites ; Crystallography, X-Ray ; Drug Evaluation, Preclinical/methods ; Ligands ; Magnetic Resonance Spectroscopy ; Proteins/chemistry
Chemical Substances	Ligands ; Proteins
Language	English
Publishing date	2007-10
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	1439176-4
ISSN	1879-0402 ; 1367-5931
ISSN (online)	1879-0402
ISSN	1367-5931
DOI	10.1016/j.cbpa.2007.07.010
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Article: The Discovery of Novel Protein Kinase Inhibitors by Using Fragment-Based High-Throughput X-ray Crystallography

Gill, Adrian / Cleasby, Anne / Jhoti, Harren

Chembiochem. 2005 Mar. 4, v. 6, no. 3

2005

Abstract: This article describes the application of a high-throughput X-ray crystallographic fragment-based screening methodology to identify low-molecular-weight leads for structure-based optimisation into protein kinase inhibitors. The identification of two ... ...

Abstract	This article describes the application of a high-throughput X-ray crystallographic fragment-based screening methodology to identify low-molecular-weight leads for structure-based optimisation into protein kinase inhibitors. The identification of two novel p38α MAP kinase inhibitors (with IC₅₀=65 and 150 nM) starting from low-molecular-weight fragments is described.
Language	English
Dates of publication	2005-0304
Size	p. 506-512.
Publishing place	Wiley-VCH Verlag
Document type	Article
ZDB-ID	2020469-3
ISSN	1439-7633 ; 1439-4227
ISSN (online)	1439-7633
ISSN	1439-4227
DOI	10.1002/cbic.200400188
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Article: The discovery of novel protein kinase inhibitors by using fragment-based high-throughput x-ray crystallography.

Gill, Adrian / Cleasby, Anne / Jhoti, Harren

Chembiochem : a European journal of chemical biology

2005 Volume 6, Issue 3, Page(s) 506–512

Abstract	This article describes the application of a high-throughput X-ray crystallographic fragment-based screening methodology to identify low-molecular-weight leads for structure-based optimisation into protein kinase inhibitors. The identification of two novel p38alpha MAP kinase inhibitors (with IC50=65 and 150 nM) starting from low-molecular-weight fragments is described.
MeSH term(s)	Crystallography, X-Ray ; Drug Evaluation, Preclinical/instrumentation ; Drug Evaluation, Preclinical/methods ; Humans ; Mitogen-Activated Protein Kinase 14/antagonists & inhibitors ; Mitogen-Activated Protein Kinase 14/chemistry ; Mitogen-Activated Protein Kinase 14/metabolism ; Peptide Fragments/antagonists & inhibitors ; Peptide Fragments/chemistry ; Peptide Fragments/metabolism ; Protein Kinase Inhibitors/chemistry ; Protein Kinase Inhibitors/pharmacology
Chemical Substances	Peptide Fragments ; Protein Kinase Inhibitors ; Mitogen-Activated Protein Kinase 14 (EC 2.7.11.24)
Language	English
Publishing date	2005-03
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	2020469-3
ISSN	1439-7633 ; 1439-4227
ISSN (online)	1439-7633
ISSN	1439-4227
DOI	10.1002/cbic.200400188
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Article ; Online: Crystal structure of Schistosoma purine nucleoside phosphorylase complexed with a novel monocyclic inhibitor.

Pereira, Humberto M / Berdini, Valério / Ferri, Mariana R / Cleasby, Anne / Garratt, Richard C

Acta tropica

2010 Volume 114, Issue 2, Page(s) 97–102

Abstract: A novel inhibitor of Schistosoma PNP was identified using an "in silico" approach allied to enzyme inhibition assays. The compound has a monocyclic structure which has not been previously described for PNP inhibitors. The crystallographic structure of ... ...

Abstract	A novel inhibitor of Schistosoma PNP was identified using an "in silico" approach allied to enzyme inhibition assays. The compound has a monocyclic structure which has not been previously described for PNP inhibitors. The crystallographic structure of the complex was determined and used to elucidate the binding mode within the active site. Furthermore, the predicted pose was very similar to that determined crystallographically, validating the methodology. The compound Sm_VS1, despite its low molecular weight, possesses an IC(50) of 1.3 microM, surprisingly low when compared with purine analogues. This is presumably due to the formation of eight hydrogen bonds with key residues in the active site E203, N245 and T244. The results of this study highlight the importance of the use of multiple conformations for the target during virtual screening. Indeed the Sm_VS1 compound was only identified after flipping the N245 side chain. It is expected that the structure will be of use in the development of new highly active non-purine based compounds against the Schistosoma enzyme.
MeSH term(s)	Animals ; Catalytic Domain ; Crystallography, X-Ray ; Enzyme Inhibitors/chemistry ; Enzyme Inhibitors/pharmacology ; Helminth Proteins/chemistry ; Inhibitory Concentration 50 ; Models, Molecular ; Molecular Structure ; Protein Binding ; Protein Structure, Tertiary ; Purine-Nucleoside Phosphorylase/antagonists & inhibitors ; Purine-Nucleoside Phosphorylase/chemistry ; Schistosoma/chemistry ; Schistosoma/enzymology
Chemical Substances	Enzyme Inhibitors ; Helminth Proteins ; Purine-Nucleoside Phosphorylase (EC 2.4.2.1)
Language	English
Publishing date	2010-05
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	210415-5
ISSN	1873-6254 ; 0001-706X
ISSN (online)	1873-6254
ISSN	0001-706X
DOI	10.1016/j.actatropica.2010.01.010
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Article: Structures for the potential drug target purine nucleoside phosphorylase from Schistosoma mansoni causal agent of schistosomiasis.

Pereira, Humberto D'Muniz / Franco, Glória Regina / Cleasby, Anne / Garratt, Richard Charles

Journal of molecular biology

2005 Volume 353, Issue 3, Page(s) 584–599

Abstract: Despite the availability of effective chemotherapy, schistosomiasis continues to be one of the major parasitic infections to affect the human population worldwide. Currently, little is known of the structural biology of the parasites that are responsible ...

Abstract	Despite the availability of effective chemotherapy, schistosomiasis continues to be one of the major parasitic infections to affect the human population worldwide. Currently, little is known of the structural biology of the parasites that are responsible for the disease and few attempts have been made to develop second generation drugs, which may become essential if resistance to those currently available becomes an issue. Here, we describe three crystal structures for the enzyme purine nucleoside phosphorylase (PNP) from Schistosoma mansoni, a component of the purine salvage pathway. PNP is known to be essential for the recovery of purine bases and nucleosides in schistosomes, due to an absence of the enzymes for de novo synthesis, making it a sensitive point in the parasite's metabolism. In all three structures reported here, acetate occupies part of the base-binding site and is directly bound to the conserved glutamic acid at position 203. One of the structures presents the crystallization additive sulfobetaine 195 (NDSB195) occupying simultaneously the ribose and phosphate binding sites, whilst a second presents only phosphate in the latter. The observation of sulfobetaine specifically bound to the protein active site was unexpected and is unique to this structure as far as we are aware. Considerable flexibility is observed in the active site, principally due to variable structural disorder in the regions centered on residues 64 and 260. This conformational plasticity extends to the way in which both NDSB195 and phosphate bind to the individual monomers of the trimeric structure reported here. Differences between the parasite and human enzymes are limited principally to the base-binding site, where the substitution of V245 in the mammalian enzymes by S247 introduces additional hydrogen bonding potential to the site. This is satisfied in the structures described here by a water molecule whose presence is normally observed only in complexes with 6-oxopurines. Residue Y202, which replaces F200 in human PNP, is able to reach over the ribose-binding site to interact with H259 and is predicted to form an additional hydrogen bond with the 5' hydroxyl of nucleoside substrates.
MeSH term(s)	Amino Acid Sequence ; Animals ; Binding Sites ; Enzyme Inhibitors/pharmacology ; Models, Molecular ; Molecular Sequence Data ; Molecular Weight ; Protein Conformation ; Purine-Nucleoside Phosphorylase/antagonists & inhibitors ; Purine-Nucleoside Phosphorylase/chemistry ; Schistosoma mansoni/drug effects ; Schistosoma mansoni/enzymology ; Schistosomiasis/parasitology ; Sequence Homology, Amino Acid
Chemical Substances	Enzyme Inhibitors ; Purine-Nucleoside Phosphorylase (EC 2.4.2.1)
Language	English
Publishing date	2005-10-28
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2005.08.045
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Article ; Online: Structure of the BTB domain of Keap1 and its interaction with the triterpenoid antagonist CDDO.

Cleasby, Anne / Yon, Jeff / Day, Philip J / Richardson, Caroline / Tickle, Ian J / Williams, Pamela A / Callahan, James F / Carr, Robin / Concha, Nestor / Kerns, Jeffrey K / Qi, Hongwei / Sweitzer, Thomas / Ward, Paris / Davies, Thomas G

PloS one

2014 Volume 9, Issue 6, Page(s) e98896

Abstract: The protein Keap1 is central to the regulation of the Nrf2-mediated cytoprotective response, and is increasingly recognized as an important target for therapeutic intervention in a range of diseases involving excessive oxidative stress and inflammation. ... ...

Abstract	The protein Keap1 is central to the regulation of the Nrf2-mediated cytoprotective response, and is increasingly recognized as an important target for therapeutic intervention in a range of diseases involving excessive oxidative stress and inflammation. The BTB domain of Keap1 plays key roles in sensing environmental electrophiles and in mediating interactions with the Cul3/Rbx1 E3 ubiquitin ligase system, and is believed to be the target for several small molecule covalent activators of the Nrf2 pathway. However, despite structural information being available for several BTB domains from related proteins, there have been no reported crystal structures of Keap1 BTB, and this has precluded a detailed understanding of its mechanism of action and interaction with antagonists. We report here the first structure of the BTB domain of Keap1, which is thought to contain the key cysteine residue responsible for interaction with electrophiles, as well as structures of the covalent complex with the antagonist CDDO/bardoxolone, and of the constitutively inactive C151W BTB mutant. In addition to providing the first structural confirmation of antagonist binding to Keap1 BTB, we also present biochemical evidence that adduction of Cys 151 by CDDO is capable of inhibiting the binding of Cul3 to Keap1, and discuss how this class of compound might exert Nrf2 activation through disruption of the BTB-Cul3 interface.
MeSH term(s)	Binding Sites ; Humans ; Imidazoles/chemistry ; Imidazoles/pharmacology ; Intracellular Signaling Peptides and Proteins/antagonists & inhibitors ; Intracellular Signaling Peptides and Proteins/chemistry ; Intracellular Signaling Peptides and Proteins/genetics ; Kelch-Like ECH-Associated Protein 1 ; Models, Molecular ; Molecular Conformation ; Mutation ; Oleanolic Acid/analogs & derivatives ; Oleanolic Acid/chemistry ; Oleanolic Acid/pharmacology ; Protein Binding ; Protein Interaction Domains and Motifs ; Structure-Activity Relationship
Chemical Substances	1-(2-cyano-3,12-dioxooleana-1,9-dien-28-oyl) imidazole ; Imidazoles ; Intracellular Signaling Peptides and Proteins ; KEAP1 protein, human ; Kelch-Like ECH-Associated Protein 1 ; Oleanolic Acid (6SMK8R7TGJ)
Language	English
Publishing date	2014-06-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0098896
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Article ; Online: Crystal structure of human soluble adenylate cyclase reveals a distinct, highly flexible allosteric bicarbonate binding pocket.

Saalau-Bethell, Susanne M / Berdini, Valerio / Cleasby, Anne / Congreve, Miles / Coyle, Joseph E / Lock, Victoria / Murray, Christopher W / O'Brien, M Alistair / Rich, Sharna J / Sambrook, Tracey / Vinkovic, Mladen / Yon, Jeff R / Jhoti, Harren

ChemMedChem

2014 Volume 9, Issue 4, Page(s) 823–832

Abstract: Soluble adenylate cyclases catalyse the synthesis of the second messenger cAMP through the cyclisation of ATP and are the only known enzymes to be directly activated by bicarbonate. Here, we report the first crystal structure of the human enzyme that ... ...

Abstract	Soluble adenylate cyclases catalyse the synthesis of the second messenger cAMP through the cyclisation of ATP and are the only known enzymes to be directly activated by bicarbonate. Here, we report the first crystal structure of the human enzyme that reveals a pseudosymmetrical arrangement of two catalytic domains to produce a single competent active site and a novel discrete bicarbonate binding pocket. Crystal structures of the apo protein, the protein in complex with α,β-methylene adenosine 5'-triphosphate (AMPCPP) and calcium, with the allosteric activator bicarbonate, and also with a number of inhibitors identified using fragment screening, all show a flexible active site that undergoes significant conformational changes on binding of ligands. The resulting nanomolar-potent inhibitors that were developed bind at both the substrate binding pocket and the allosteric site, and can be used as chemical probes to further elucidate the function of this protein.
MeSH term(s)	Adenylyl Cyclase Inhibitors ; Adenylyl Cyclases/chemistry ; Adenylyl Cyclases/metabolism ; Bicarbonates/chemical synthesis ; Bicarbonates/chemistry ; Bicarbonates/pharmacology ; Catalytic Domain/drug effects ; Crystallography, X-Ray ; Dose-Response Relationship, Drug ; Enzyme Activation/drug effects ; Enzyme Inhibitors/chemical synthesis ; Enzyme Inhibitors/chemistry ; Enzyme Inhibitors/pharmacology ; Humans ; Models, Molecular ; Structure-Activity Relationship
Chemical Substances	Adenylyl Cyclase Inhibitors ; Bicarbonates ; Enzyme Inhibitors ; ADCY10 protein, human (EC 4.6.1.1) ; Adenylyl Cyclases (EC 4.6.1.1)
Language	English
Publishing date	2014-02-24
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2218496-X
ISSN	1860-7187 ; 1860-7179
ISSN (online)	1860-7187
ISSN	1860-7179
DOI	10.1002/cmdc.201300480
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