4E3F | pdb_00004e3f

Nucleophile recognition as an alternative inhibition mode for benzoic acid based carbonic anhydrase inhibitors

• PDB DOI: https://doi.org/10.2210/pdb4E3F/pdb

• Classification: LYASE/LYASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-03-09 Released: 2012-06-27 
• Deposition Author(s): Cohen, S.M., Martin, D.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.204 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

Nucleophile recognition as an alternative inhibition mode for benzoic acid based carbonic anhydrase inhibitors

Martin, D.P., Cohen, S.M.

(2012) Chem Commun (Camb) 48: 5259-5261

• PubMed: 22531842 
• DOI: https://doi.org/10.1039/c2cc32013d
• Primary Citation Related Structures: 
  4E3D, 4E3F, 4E3G, 4E3H, 4E49, 4E4A


• PubMed Abstract: 
  

  A series of hydroxybenzoic acid derivatives have shown inhibitory activity against carbonic anhydrase (CA). X-ray crystallography shows that these molecules inhibit not by binding the active site metal ion but by strong hydrogen bonding to the metal-bound water nucleophile. The binding mode observed for these molecules is distinct when compared to other non-metal-binding CA inhibitors.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, USA.

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: 30.14 kDa 
• Atom Count: 2,290 
• Modeled Residue Count: 257 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	260	Homo sapiens	Mutation(s): 0  Gene Names: CA2 EC: 4.2.1.1 (PDB Primary Data), 4.2.1.69 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00918 (Homo sapiens) Explore P00918  Go to UniProtKB:  P00918
PHAROS:  P00918 GTEx:  ENSG00000104267

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MBO	C [auth A]	MERCURIBENZOIC ACID C7 H5 Hg O2 FVFZSVRSDNUCGG-UHFFFAOYSA-N
GRE	D [auth A], E [auth A], F [auth A]	2,6-DIHYDROXYBENZOIC ACID C7 H6 O4 AKEUNCKRJATALU-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
GRE	BindingDB:  4E3F	Ki: 5200 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.204 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.273	α = 90
b = 41.407	β = 104.23
c = 72.227	γ = 90

Software Package:

Software Name	Purpose
APEX	data collection
PHASER	phasing
REFMAC	refinement
APEX	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-27 
Deposition Author(s): Cohen, S.M., Martin, D.P.

Revision History  

• Version 1.0: 2012-06-27
  Type: Initial release
  
• Version 1.1: 2018-03-21
  Changes: Data collection
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description