2RFH

Crystal Structure Analysis of CPA-2-benzyl-3-nitropropanoic acid complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Nitro as a novel zinc-binding group in the inhibition of carboxypeptidase A

Wang, S.-H.Wang, S.-F.Xuan, W.Zeng, Z.-H.Jin, J.-Y.Ma, J.Tian, G.R.

(2008) Bioorg Med Chem 16: 3596-3601

  • DOI: 10.1016/j.bmc.2008.02.010
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • 2-Substituted 3-nitropropanoic acids were designed and synthesized as inhibitors against carboxypeptidase A (CPA). (R)-2-Benzyl- 3-nitropropanoic acid showed a potent inhibition against CPA (K(i)=0.15 microM). X-ray crystallography discloses that the ...

    2-Substituted 3-nitropropanoic acids were designed and synthesized as inhibitors against carboxypeptidase A (CPA). (R)-2-Benzyl- 3-nitropropanoic acid showed a potent inhibition against CPA (K(i)=0.15 microM). X-ray crystallography discloses that the nitro group well mimics the transition state occurred in the hydrolysis catalyzed by CPA, that is, an O,O'-bidentate coordination to the zinc ion and the two respective hydrogen bonds with Glu-270 and Arg-127. Because the nitro group is a planar species, we proposed (R)-2-benzyl-3-nitropropanoic acid as a pseudo-transition-state analog inhibitor against CPA.


    Organizational Affiliation

    Department of Chemistry, Yanbian University, Yanji, Jilin 133002, China.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carboxypeptidase A1
A
307N/AMutation(s): 0 
EC: 3.4.17.1
Find proteins for P00730 (Bos taurus)
Go to UniProtKB:  P00730
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
23N
Query on 23N

Download CCD File 
A
(2R)-2-benzyl-3-nitropropanoic acid
C10 H11 N O4
GCXOTBPCUQHSAO-SECBINFHSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
23NKi:  150   nM  Binding MOAD
23NKi :  150   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.297α = 90
b = 62.698β = 96.99
c = 48.974γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALAdata scaling
CCP4phasing
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-04-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance