5J8Z

Human carbonic anhydrase II in complex with ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Kinetic and X-ray crystallographic investigations of substituted 2-thio-6-oxo-1,6-dihydropyrimidine-benzenesulfonamides acting as carbonic anhydrase inhibitors.

Vullo, D.Supuran, C.T.Scozzafava, A.De Simone, G.Monti, S.M.Alterio, V.Carta, F.

(2016) Bioorg Med Chem 24: 3643-3648

  • DOI: 10.1016/j.bmc.2016.06.005
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Herein we report an in vitro kinetic evaluation against the most relevant human carbonic anhydrase (hCA, EC 4.2.1.1) isoforms (I, II, IX and XII) of a small series of lactate dehydrogenase (LDH, EC 1.1.1.27) inhibitors. All compounds contain a primar ...

    Herein we report an in vitro kinetic evaluation against the most relevant human carbonic anhydrase (hCA, EC 4.2.1.1) isoforms (I, II, IX and XII) of a small series of lactate dehydrogenase (LDH, EC 1.1.1.27) inhibitors. All compounds contain a primary sulfonamide zinc-binding group (ZBG) substituted with the 2-thio-6-oxo-1,6-dihydropyrimidine scaffold. By means of X-ray crystallographic experiments we explored the ligand-enzyme binding modes, thus highlighting the contribution of the 2-thio-6-oxo-1,6-dihydropyrimidine moiety to the stabilization of the complex.


    Organizational Affiliation

    Università degli Studi di Firenze, Dipartimento di Chimica, Laboratorio di Chimica Bioinorganica, Rm. 188, Via della Lastruccia 3, 50019 Sesto Fiorentino (Florence), Italy. Electronic address: fabrizio.carta@unifi.it.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carbonic anhydrase 2
A
262Homo 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
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FC4
Query on FC4

Download CCD File 
A
(2R)-2-{[4-(4-chlorophenyl)-5-cyano-6-oxo-1,6-dihydropyrimidin-2-yl]sulfanyl}-N-(4-sulfamoylphenyl)propanamide
C20 H16 Cl N5 O4 S2
JDIGFAGHWNBGPU-LLVKDONJSA-N
 Ligand Interaction
6KE
Query on 6KE

Download CCD File 
A
(2S)-2-{[4-(4-chlorophenyl)-5-cyano-6-oxo-1,6-dihydropyrimidin-2-yl]sulfanyl}-N-(4-sulfamoylphenyl)propanamide
C20 H16 Cl N5 O4 S2
JDIGFAGHWNBGPU-NSHDSACASA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 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 %)
FC4Ki:  5   nM  Binding MOAD
6KEKi:  5   nM  Binding MOAD
6KEKi:  5   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.162 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.396α = 90
b = 41.39β = 104.24
c = 71.823γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-06-29
    Type: Initial release
  • Version 1.1: 2016-07-27
    Changes: Database references