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 

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Ligand Structure Quality Assessment 


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: https://doi.org/10.1016/j.bmc.2008.02.010
  • Primary Citation of Related Structures:  
    2RFH

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carboxypeptidase A1307Bos taurusMutation(s): 0 
EC: 3.4.17.1
UniProt
Find proteins for P00730 (Bos taurus)
Explore P00730 
Go to UniProtKB:  P00730
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00730
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
23N
Query on 23N

Download Ideal Coordinates CCD File 
C [auth A](2R)-2-benzyl-3-nitropropanoic acid
C10 H11 N O4
GCXOTBPCUQHSAO-SECBINFHSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
23N Binding MOAD:  2RFH Ki: 150 (nM) from 1 assay(s)
PDBBind:  2RFH Ki: 150 (nM) from 1 assay(s)
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

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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