3P5L

Human Carbonic Anhydrase complexed with sodium 4-cyano-4-phenylpiperidine-1-carbodithioate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.498 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1039/c2cc16395k
  • Primary Citation of Related Structures:  3P58

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carbonic anhydrase 2
A
260Homo 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
IT5
Query on IT5

Download SDF File 
Download CCD File 
A
4-cyano-4-phenylpiperidine-1-carbodithioic acid
C13 H14 N2 S2
GPPHSVWKEUXGQQ-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IT5Ki: 40.8 nM BINDINGMOAD
IT5Ki: 40.8 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.498 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.166 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.325α = 90.00
b = 41.310β = 104.45
c = 72.169γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
CrystalCleardata collection
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-10-19
    Type: Initial release
  • Version 1.1: 2012-01-25
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Refinement description