4QY3

THE CRYSTAL STRUCTURE OF THE COMPLEX of HCAII WITH AN ORTHO-SUBSTITUTED BENZOIC ACID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.163 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Out of the active site binding pocket for carbonic anhydrase inhibitors.

D'Ambrosio, K.Carradori, S.Monti, S.M.Buonanno, M.Secci, D.Vullo, D.Supuran, C.T.De Simone, G.

(2014) Chem Commun (Camb) 51: 302-305

  • DOI: 10.1039/c4cc07320g
  • Primary Citation of Related Structures:  
    4QY3

  • PubMed Abstract: 
  • A structural study of the adduct which 2-benzylsulfinylbenzoic acid forms with human carbonic anhydrase II is reported, showing a binding mode completely different from any other class of carbonic anhydrase inhibitors investigated so far; this carboxylate binds in a pocket situated out of the enzyme active site ...

    A structural study of the adduct which 2-benzylsulfinylbenzoic acid forms with human carbonic anhydrase II is reported, showing a binding mode completely different from any other class of carbonic anhydrase inhibitors investigated so far; this carboxylate binds in a pocket situated out of the enzyme active site.


    Organizational Affiliation

    Istituto di Biostrutture e Bioimmagini-CNR, Via Mezzocannone 16, 80134, Naples, Italy. gdesimon@unina.it katia.dambrosio@cnr.it.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Carbonic anhydrase 2A259Homo sapiensMutation(s): 0 
Gene Names: CA2
EC: 4.2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P00918 (Homo sapiens)
Explore P00918 
Go to UniProtKB:  P00918
PHAROS:  P00918
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HGB (Subject of Investigation/LOI)
Query on HGB

Download Ideal Coordinates CCD File 
D [auth A]4-(HYDROXYMERCURY)BENZOIC ACID
C7 H6 Hg O3
WMHRYLDWLOGHSG-UHFFFAOYSA-M
 Ligand Interaction
3G1 (Subject of Investigation/LOI)
Query on 3G1

Download Ideal Coordinates CCD File 
C [auth A]2-[(S)-benzylsulfinyl]benzoic acid
C14 H12 O3 S
IHSDWNKZUMUWEX-SFHVURJKSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
3G1 Binding MOAD:  4QY3 Ki: 150 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.163 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.15α = 90
b = 41.53β = 104.52
c = 72.18γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-03
    Type: Initial release
  • Version 1.1: 2014-12-17
    Changes: Database references