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 2OAZ | pdb_00002oaz

Human Methionine Aminopeptidase-2 Complexed with SB-587094


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.287 (Depositor) 
  • R-Value Work: 
    0.255 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2OAZ

This is version 1.5 of the entry. See complete history. 

Literature

Highly potent inhibitors of methionine aminopeptidase-2 based on a 1,2,4-triazole pharmacophore.

Marino, J.P., Fisher, P.W., Hofmann, G.A., Kirkpatrick, R.B., Janson, C.A., Johnson, R.K., Ma, C., Mattern, M., Meek, T.D., Ryan, M.D., Schulz, C., Smith, W.W., Tew, D.G., Tomazek, T.A., Veber, D.F., Xiong, W.C., Yamamoto, Y., Yamashita, K., Yang, G., Thompson, S.K.

(2007) J Med Chem 50: 3777-3785

  • DOI: https://doi.org/10.1021/jm061182w
  • Primary Citation Related Structures: 
    2OAZ

  • PubMed Abstract: 

    High-throughput screening for inhibitors of the human metalloprotease, methionine aminopeptidase-2 (MetAP2), identified a potent class of 3-anilino-5-benzylthio-1,2,4-triazole compounds. Efficient array and interative synthesis of triazoles led to rapid SAR development around the aniline, benzylthio, and triazole moeities. Evaluation of these analogs in a human MetAP2 enzyme assay led to the identification of several inhibitors with potencies in the 50-100 picomolar range. The deleterious effects on inhibitor potency by methylation of the anilino-triazole nitrogens, as well as the X-ray crystal structure of triazole 102 bound in the active site of MetAP2, confirm the key interactions between the triazole nitrogens, the active site cobalt atoms, and the His-231 side-chain. The structure has also provided a rationale for interpreting SAR within the triazole series. Key aniline (2-isopropylphenyl) and sulfur substituents (furanylmethyl) identified in the SAR studies led to the identification of potent inhibitors (103 and 104) of endothelial cell proliferation. Triazoles 103 and 104 also exhibited dose-dependent activity in an aortic ring tissue model of angiogenesis highlighting the potential utility of MetAP2 inhibitors as anticancer agents.


  • Organizational Affiliation: 
    • Department of Medicinal Chemistry, Enzymology, Oncology, and Structural Biology, GlaxoSmithkline, King of Prussia, PA 19406, USA. joseph.p.marino@gsk.com

Macromolecule Content 

  • Total Structure Weight: 41.82 kDa 
  • Atom Count: 3,115 
  • Modeled Residue Count: 355 
  • Deposited Residue Count: 369 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
human Methionine Amino Peptidase 2369Homo sapiensMutation(s): 1 
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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50579
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
I96

Query on I96



Download:Ideal Coordinates CCD File
D [auth A]N-(2-ISOPROPYLPHENYL)-3-[(2-THIENYLMETHYL)THIO]-1H-1,2,4-TRIAZOL-5-AMINE
C16 H18 N4 S2
QMNSHLAPQLBIGP-UHFFFAOYSA-N
CO

Query on CO



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A]
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.287 (Depositor) 
  • R-Value Work:  0.255 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.698α = 90
b = 99.217β = 90
c = 101.304γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2007-06-19
    Type: Initial release
  • Version 1.1: 2008-01-14
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-12-27
    Changes: Data collection
  • Version 1.5: 2024-11-20
    Changes: Structure summary