1R5G

Crystal Structure of MetAP2 complexed with A311263

• PDB DOI: https://doi.org/10.2210/pdb1R5G/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2003-10-10 Released: 2004-10-12 
• Deposition Author(s): Sheppard, G.S., Wang, J., Kawai, M., BaMaung, N.Y., Craig, R.A., Erickson, S.A., Lynch, L., Patel, J., Yang, F., Searle, X.B., Lou, P., Park, C., Kim, K.H., Henkin, J., Lesniewski, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.259 (Depositor) 
• R-Value Work: 
  0.201 (Depositor), 0.216 (DCC) 

Literature

3-Amino-2-hydroxyamides and related compounds as inhibitors of methionine aminopeptidase-2.

Sheppard, G.S., Wang, J., Kawai, M., BaMaung, N.Y., Craig, R.A., Erickson, S.A., Lynch, L., Patel, J., Yang, F., Searle, X.B., Lou, P., Park, C., Kim, K.H., Henkin, J., Lesniewski, R.

(2004) Bioorg Med Chem Lett 14: 865-868

• PubMed: 15012983 
• DOI: https://doi.org/10.1016/j.bmcl.2003.12.031
• Primary Citation of Related Structures:  
  1R58, 1R5G, 1R5H


• PubMed Abstract: 
  

  Substituted 3-amino-2-hydroxyamides and related hydroxyamides and acylhydrazines were identified as inhibitors of human methionine aminopeptidase-2 (MetAP2). Examination of substituents through parallel synthesis and iterative structure-based design allowed the identification of potent inhibitors with good selectivity against MetAP1. Diacylhydrazine 3t (A-357300) was identified as an analogue displaying inhibition of methionine processing and cellular proliferation in human microvascular endothelial cells (HMVEC).

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Organizational Affiliation: 

Abbott Laboratories, Global Pharmaceutical Research and Development, Cancer Research, 100 Abbott Park Road, Abbott Park, IL 60064, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 41.83 kDa 
• Atom Count: 3,357 
• Modelled Residue Count: 369 
• Deposited Residue Count: 369 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine aminopeptidase 2	A	369	Homo sapiens	Mutation(s): 0  EC: 3.4.11.18
UniProt & NIH Common Fund Data Resources
Find proteins for P50579 (Homo sapiens) Explore P50579  Go to UniProtKB:  P50579
PHAROS:  P50579 GTEx:  ENSG00000111142

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AO1	D [auth A]	(2S,3R)-3-AMINO-2-HYDROXY-5-(ETHYLSULFANYL)PENTANOYL-((S)-(-)-(1-NAPHTHYL)ETHYL)AMIDE C19 H26 N2 O2 S AIIOXZPEXXZCML-KKXDTOCCSA-N
MN	B [auth A], C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
AO1	BindingDB:  1R5G	IC50: min: 22, max: 30 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.259 (Depositor) 
• R-Value Work:  0.201 (Depositor), 0.216 (DCC) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.009	α = 90
b = 98.612	β = 90
c = 101.093	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-10-12 
Deposition Author(s): Sheppard, G.S., Wang, J., Kawai, M., BaMaung, N.Y., Craig, R.A., Erickson, S.A., Lynch, L., Patel, J., Yang, F., Searle, X.B., Lou, P., Park, C., Kim, K.H., Henkin, J., Lesniewski, R.

Revision History  

• Version 1.0: 2004-10-12
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2024-10-16
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary