2ADU

Human Methionine Aminopeptidase Complex with 4-Aryl-1,2,3-triazole Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2ADU/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2005-07-20 Released: 2005-09-13 
• Deposition Author(s): Kallander, L.S., Lu, Q., Chen, W., Tomaszek, T., Yang, G., Tew, D., Meek, T.D., Hofmann, G.A., Schulz-Pritchard, C.K., Smith, W.W., Janson, C.A., Ryan, M.D., Zhang, G.F., Johanson, K.O., Kirkpatrick, R.B., Ho, T.F., Fisher, P.W., Mattern, M.R., Johnson, R.K., Hansbury, M.J., Winkler, J.D., Ward, K.W., Veber, D.F., Thompson, S.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.355 (Depositor) 
• R-Value Work: 
  0.335 (Depositor) 
• R-Value Observed: 
  0.335 (Depositor) 

Starting Model: experimental

Literature

4-Aryl-1,2,3-triazole: A Novel Template for a Reversible Methionine Aminopeptidase 2 Inhibitor, Optimized To Inhibit Angiogenesis in Vivo

Kallander, L.S., Lu, Q., Chen, W., Tomaszek, T., Yang, G., Tew, D., Meek, T.D., Hofmann, G.A., Schulz-Pritchard, C.K., Smith, W.W., Janson, C.A., Ryan, M.D., Zhang, G.F., Johanson, K.O., Kirkpatrick, R.B., Ho, T.F., Fisher, P.W., Mattern, M.R., Johnson, R.K., Hansbury, M.J., Winkler, J.D., Ward, K.W., Veber, D.F., Thompson, S.K.

(2005) J Med Chem 48: 5644-5647

• PubMed: 16134930 
• DOI: https://doi.org/10.1021/jm050408c
• Primary Citation of Related Structures:  
  2ADU


• PubMed Abstract: 
  

  Inhibitors of human methionine aminopeptidase type 2 (hMetAP2) are of interest as potential treatments for cancer. A new class of small molecule reversible inhibitors of hMetAP2 was discovered and optimized, the 4-aryl-1,2,3-triazoles. Compound 24, a potent inhibitor of cobalt-activated hMetAP2, also inhibits human and mouse endothelial cell growth. Using a mouse matrigel model, this reversible hMetAP2 inhibitor was also shown to inhibit angiogenesis in vivo.

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Organizational Affiliation: 

GlaxoSmithKline Pharmaceuticals, King of Prussia, Pennsylvania 19406, 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: 41.65 kDa 
• Atom Count: 3,107 
• Modelled Residue Count: 355 
• 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  Gene Names: METAP2, MNPEP, P67EIF2 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
R20	D [auth A]	4-(3-METHYLPHENYL)-1H-1,2,3-TRIAZOLE C9 H9 N3 XQHCBHNLRWLGQS-UHFFFAOYSA-N
CO	B [auth A], C [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
R20	BindingDB:  2ADU	Ki: 18 (nM) from 1 assay(s)
		IC50: 18 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.355 (Depositor) 
• R-Value Work:  0.335 (Depositor) 
• R-Value Observed: 0.335 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.819	α = 90
b = 99.264	β = 90
c = 101.282	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-09-13 
Deposition Author(s): Kallander, L.S., Lu, Q., Chen, W., Tomaszek, T., Yang, G., Tew, D., Meek, T.D., Hofmann, G.A., Schulz-Pritchard, C.K., Smith, W.W., Janson, C.A., Ryan, M.D., Zhang, G.F., Johanson, K.O., Kirkpatrick, R.B., Ho, T.F., Fisher, P.W., Mattern, M.R., Johnson, R.K., Hansbury, M.J., Winkler, J.D., Ward, K.W., Veber, D.F., Thompson, S.K.

Revision History  

• Version 1.0: 2005-09-13
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-10-30
  Changes: Structure summary