6G3Q | pdb_00006g3q

Crystal structure of human carbonic anhydrase II in complex with the inhibitor famotidine

• PDB DOI: https://doi.org/10.2210/pdb6G3Q/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2018-03-26 Released: 2018-11-28 
• Deposition Author(s): Ferraroni, M., Supuran, C.T., Angeli, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.01 Å
• R-Value Free: 
  0.151 (Depositor), 0.151 (DCC) 
• R-Value Work: 
  0.127 (Depositor), 0.127 (DCC) 
• R-Value Observed: 
  0.128 (Depositor) 

Starting Model: experimental

Literature

Famotidine, an Antiulcer Agent, Strongly InhibitsHelicobacter pyloriand Human Carbonic Anhydrases.

Angeli, A., Ferraroni, M., Supuran, C.T.

(2018) ACS Med Chem Lett 9: 1035-1038

• PubMed: 30344913 
• DOI: https://doi.org/10.1021/acsmedchemlett.8b00334
• Primary Citation Related Structures: 
  6G3Q, 6G3V


• PubMed Abstract: 
  

  Famotidine, an antiulcer drug incorporating a sulfamide motif, was investigated as carbonic anhydrase inhibitor (CAI). It acts as a nanomolar inhibitor of several human (hCA II, VI, VII and XII) and Helicobacter pylori CAs. The high resolution X-ray structures of famotidine bound to hCA I and II revealed interesting aspects related to its CA inhibition mechanism, offering the possibility to develop antibacterials with a novel mechanism of action.

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Organizational Affiliation: 
• University of Florence, NEUROFARBA Dept., Sezione di Scienze Farmaceutiche, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy.
University of Florence, Department of Chemistry "Ugo Schiff", Via della Lastruccia 13, I-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: 29.79 kDa 
• Atom Count: 2,682 
• Modeled Residue Count: 260 
• 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  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
FO9 (Subject of Investigation/LOI)	C [auth A]	famotidine C8 H17 N7 O2 S3 YFGRAZUYIUBWJO-UHFFFAOYSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.01 Å
• R-Value Free:  0.151 (Depositor), 0.151 (DCC) 
• R-Value Work:  0.127 (Depositor), 0.127 (DCC) 
• R-Value Observed: 0.128 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.316	α = 90
b = 41.439	β = 104.34
c = 72.112	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-11-28 
Deposition Author(s): Ferraroni, M., Supuran, C.T., Angeli, A.

Revision History  

• Version 1.0: 2018-11-28
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2025-10-01
  Changes: Derived calculations, Structure summary