3P58

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

• PDB DOI: https://doi.org/10.2210/pdb3P58/pdb

• Classification: lyase/inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-10-08 Released: 2011-10-19 
• Deposition Author(s): Aggarwal, M., McKenna, R.

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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 

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

• PubMed: 22218610 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 29.55 kDa 
• Atom Count: 2,418 
• Modelled Residue Count: 257 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	260	Homo sapiens	Mutation(s): 0  Gene Names: CA2 EC: 4.2.1.1 (PDB Primary Data), 4.2.1.69 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00918 (Homo sapiens) Explore P00918  Go to UniProtKB:  P00918
PHAROS:  P00918 GTEx:  ENSG00000104267

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P58	C [auth A]	benzyl(methyl)carbamodithioic acid C9 H11 N S2 KVRJHAJGPHILSK-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
P58	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 = 42.23	α = 90
b = 41.125	β = 104.39
c = 71.897	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-10-19 
Deposition Author(s): Aggarwal, M., McKenna, R.

Revision History  

• 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