2EA4 | pdb_00002ea4

h-MetAP2 complexed with A797859

• PDB DOI: https://doi.org/10.2210/pdb2EA4/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-01-30 Released: 2008-02-05 
• Deposition Author(s): Park, C.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.272 (Depositor) 
• R-Value Work: 
  0.211 (Depositor) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

Literature

Lead optimization of methionine aminopeptidase-2 (MetAP2) inhibitors containing sulfonamides of 5,6-disubstituted anthranilic acids

Wang, G.T., Mantei, R.A., Kawai, M., Tedrow, J.S., Barnes, D.M., Wang, J., Zhang, Q., Lou, P., Garcia, L.A., Bouska, J., Yates, M., Park, C., Judge, R.A., Lesniewski, R., Sheppard, G.S., Bell, R.L.

(2007) Bioorg Med Chem Lett 17: 2817-2822

• PubMed: 17350258 
• DOI: https://doi.org/10.1016/j.bmcl.2007.02.062
• Primary Citation Related Structures: 
  2EA2, 2EA4


• PubMed Abstract: 
  

  A series of aryl sulfonamides of 5,6-disubstituted anthranilic acids were identified as potent inhibitors of methionine aminopeptidase-2 (MetAP2). Small alkyl groups and 3-furyl were tolerated at the 5-position of anthranilic acid, while -OCH(3), CH(3), and Cl were found optimal for the 6-position. Placement of 2-aminoethoxy group at the 6-position enabled interaction with the second Mn(2+) but did not result in enhancement in potency. Introduction of a tertiary amino moiety at the ortho-position of the sulfonyl phenyl ring gave reduced protein binding and improved cellular activity, but led to lower oral bioavailability.

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Organizational Affiliation: 
• Cancer Research, Global Pharmaceutical Research & Development, Abbott Laboratories, 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: 41.86 kDa 
• Atom Count: 3,252 
• Modeled 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
F79	D [auth A]	2-(2-AMINOETHOXY)-3-ETHYL-6-{[(4-FLUOROPHENYL)SULFONYL]AMINO}BENZOIC ACID C17 H19 F N2 O5 S YLNWNNUWISTBAA-UHFFFAOYSA-N
MN	B [auth A], C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
F79	BindingDB:  2EA4	IC50: 46 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.272 (Depositor) 
• R-Value Work:  0.211 (Depositor) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.091	α = 90
b = 100.28	β = 90
c = 100.722	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-02-05 
Deposition Author(s): Park, C.H.

Revision History  

• Version 1.0: 2008-02-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary