2RFH | pdb_00002rfh

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

• PDB DOI: https://doi.org/10.2210/pdb2RFH/pdb

• Classification: HYDROLASE
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 2007-09-29 Released: 2008-04-22 
• Deposition Author(s): Wang, S.-F., Zeng, Z.-H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.227 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

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

• PubMed: 18289863 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 34.72 kDa 
• Atom Count: 2,650 
• Modelled Residue Count: 307 
• Deposited Residue Count: 307 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carboxypeptidase A1	A	307	Bos taurus	Mutation(s): 0  EC: 3.4.17.1
UniProt
Find proteins for P00730 (Bos taurus) Explore P00730  Go to UniProtKB:  P00730

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
23N	C [auth A]	(2R)-2-benzyl-3-nitropropanoic acid C10 H11 N O4 GCXOTBPCUQHSAO-SECBINFHSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.227 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.297	α = 90
b = 62.698	β = 96.99
c = 48.974	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SCALA	data scaling
CCP4	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-22 
Deposition Author(s): Wang, S.-F., Zeng, Z.-H.

Revision History  

• Version 1.0: 2008-04-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary