3P58

Human Carbonic Anhydrase in complex with Benzyl (Methyl) Carbamodithoic Acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.151 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Dithiocarbamates: a new class of carbonic anhydrase inhibitors. Crystallographic and kinetic investigations.

Carta, F.Aggarwal, M.Maresca, A.Scozzafava, A.McKenna, R.Supuran, C.T.

(2012) Chem Commun (Camb) 48: 1868-1870

  • DOI: https://doi.org/10.1039/c2cc16395k
  • Primary Citation of Related Structures:  
    3P58, 3P5L

  • PubMed Abstract: 

    The zinc enzyme carbonic anhydrase (CA, EC 4.2.1.1) is inhibited by several classes of zinc-binders (sulfonamides, sulfamates, and sulfamides) as well as by compounds which do not interact with the metal ion (phenols, polyamines and coumarins). Here we report a new class of potent CA inhibitors which bind the zinc ion: the dithiocarbamates (DTCs). They coordinate to the zinc ion from the enzyme active site in monodentate manner and establish many favorable interactions with amino acid residues nearby. Several low nanomolar CA I, II and IX inhibitors were detected.


  • Organizational Affiliation

    Università degli Studi di Firenze, Laboratorio di Chimica Bioinorganica, Rm. 188, Via della Lastruccia 3, I-50019 Sesto Fiorentino (Firenze), Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbonic anhydrase 2260Homo 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
GTEx:  ENSG00000104267 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00918
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P58
Query on P58

Download Ideal Coordinates CCD File 
C [auth A]benzyl(methyl)carbamodithioic acid
C9 H11 N S2
KVRJHAJGPHILSK-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
P58 Binding MOAD:  3P58 Ki: 25.4 (nM) from 1 assay(s)
PDBBind:  3P58 Ki: 25.4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.151 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.23α = 90
b = 41.125β = 104.39
c = 71.897γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-19
    Type: Initial release
  • Version 1.1: 2012-01-25
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Advisory, Refinement description
  • Version 1.3: 2024-02-21
    Changes: Advisory, Data collection, Database references, Derived calculations