3M1K

Carbonic Anhydrase in complex with fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.122 
  • R-Value Observed: 0.128 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Bidentate Zinc chelators for alpha-carbonic anhydrases that produce a trigonal bipyramidal coordination geometry.

Schulze Wischeler, J.Innocenti, A.Vullo, D.Agrawal, A.Cohen, S.M.Heine, A.Supuran, C.T.Klebe, G.

(2010) ChemMedChem 5: 1609-1615

  • DOI: 10.1002/cmdc.201000200
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • A series of new zinc binding groups (ZBGs) has been evaluated kinetically on 13 carbonic anhydrase (CA) isoforms. The fragments show affinity for all isoforms with IC(50) values in the range of 2-11 microM. The crystal structure of hCA II in complex ...

    A series of new zinc binding groups (ZBGs) has been evaluated kinetically on 13 carbonic anhydrase (CA) isoforms. The fragments show affinity for all isoforms with IC(50) values in the range of 2-11 microM. The crystal structure of hCA II in complex with one such fragment reveals a bidentate binding mode with a trigonal-bipyramidal coordination geometry at the Zn(2+) center. The fragment also interacts with Thr199 and Thr200 through hydrogen bonding and participates in a water network. Further development of this ZBG should increase the binding affinity leading to a structurally distinct and promising class of CA inhibitors.


    Organizational Affiliation

    Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carbonic anhydrase 2
A
265Homo sapiensMutation(s): 0 
Gene Names: CA2
EC: 4.2.1.1
Find proteins for P00918 (Homo sapiens)
Go to UniProtKB:  P00918
NIH Common Fund Data Resources
PHAROS  P00918
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BE7
Query on BE7

Download CCD File 
A
(4-CARBOXYPHENYL)(CHLORO)MERCURY
C7 H5 Cl Hg O2
YFZOUMNUDGGHIW-UHFFFAOYSA-M
 Ligand Interaction
BEW
Query on BEW

Download CCD File 
A
1-hydroxy-2-sulfanylpyridinium
C5 H6 N O S
YBBJKCMMCRQZMA-UHFFFAOYSA-O
 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 %)
BEWKi:  4100   nM  Binding MOAD
BEWKi :  4100   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.122 
  • R-Value Observed: 0.128 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.3α = 90
b = 41.4β = 104.4
c = 72.4γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
CNSrefinement
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-11-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2019-07-17
    Changes: Data collection, Refinement description