3P5A | pdb_00003p5a

Human Carbonic Anhydrase complexed with Sodium morpholinocarbodithioate

• PDB DOI: https://doi.org/10.2210/pdb3P5A/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: 
  0.169 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.149 (DCC) 
• R-Value Observed: 
  0.149 (Depositor) 

Literature

Dithiocarbamates strongly inhibit carbonic anhydrases and show antiglaucoma action in vivo

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

(2012) J Med Chem 55: 1721-1730

• PubMed: 22276570 
• DOI: https://doi.org/10.1021/jm300031j
• Primary Citation Related Structures: 
  3P5A


• PubMed Abstract: 
  

  A series of dithiocarbamates were prepared by reaction of primary/secondary amines with carbon disulfide in the presence of bases. These compounds were tested for the inhibition of four human (h) isoforms of the zinc enzyme carbonic anhydrase, CA (EC 4.2.1.1), hCA I, II, IX, and XII, involved in pathologies such as glaucoma (CA II and XII) or cancer (CA IX). Several low nanomolar inhibitors targeting these CAs were detected. The X-ray crystal structure of the hCA II adduct with morpholine dithiocarbamate evidenced the inhibition mechanism of these compounds, which coordinate to the metal ion through a sulfur atom from the dithiocarbamate zinc-binding function. Some dithiocarbamates showed an effective intraocular pressure lowering activity in an animal model of glucoma.

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Organizational Affiliation: 
• Laboratorio di Chimica Bioinorganica, Polo Scientifico, Università degli Studi di Firenze, Room 188, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, 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: 29.6 kDa 
• Atom Count: 2,392 
• Modeled 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IT2	C [auth A]	morpholine-4-carbodithioic acid C5 H9 N O S2 NRMQMTQTYONMFY-UHFFFAOYSA-N
DMS	D [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free:  0.169 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.149 (DCC) 
• R-Value Observed: 0.149 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.262	α = 90
b = 41.21	β = 104.21
c = 72.151	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: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations