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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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

  • 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 sapiensGene Names: CA2
EC: 4.2.1.1
Find proteins for P00918 (Homo sapiens)
Go to Gene View: CA2
Go to UniProtKB:  P00918
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
BEW
Query on BEW

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Download CCD File 
A
1-hydroxy-2-sulfanylpyridinium
C5 H6 N O S
YBBJKCMMCRQZMA-UHFFFAOYSA-O
 Ligand Interaction
BE7
Query on BE7

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Download CCD File 
A
(4-CARBOXYPHENYL)(CHLORO)MERCURY
P-CHLOROMERCURIBENZOIC ACID
C7 H5 Cl Hg O2
YFZOUMNUDGGHIW-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BEWKi: 4100 nM BINDINGMOAD
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 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.300α = 90.00
b = 41.400β = 104.40
c = 72.400γ = 90.00
Software Package:
Software NamePurpose
SHELXL-97refinement
HKL-2000data reduction
CNSrefinement
MAR345data collection
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-11-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Refinement description