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 

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Ligand Structure Quality Assessment 


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
  • Primary Citation of Related Structures:  
    5J8Z

  • 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 primary sulfonamide zinc-binding group (ZBG) substituted with the 2-thio-6-oxo-1,6-dihydropyrimidine scaffold ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Carbonic anhydrase 2A262Homo 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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6KE (Subject of Investigation/LOI)
Query on 6KE

Download Ideal Coordinates CCD File 
E [auth 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
FC4 (Subject of Investigation/LOI)
Query on FC4

Download Ideal Coordinates CCD File 
D [auth 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
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-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
FC4 Binding MOAD:  5J8Z Ki: 5 (nM) from 1 assay(s)
6KE Binding MOAD:  5J8Z Ki: 5 (nM) from 1 assay(s)
BindingDB:  5J8Z Ki: 5 (nM) from 1 assay(s)
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

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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