6G3Q

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.01 Å
  • R-Value Free: 0.151 
  • R-Value Work: 0.127 
  • R-Value Observed: 0.128 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


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

  • DOI: 10.1021/acsmedchemlett.8b00334
  • Primary Citation of 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 ...

    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.


    Organizational Affiliation

    University of Florence, NEUROFARBA Dept., Sezione di Scienze Farmaceutiche, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Carbonic anhydrase 2A260Homo 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FO9 (Subject of Investigation/LOI)
Query on FO9

Download Ideal Coordinates CCD File 
C [auth A]famotidine
C8 H17 N7 O2 S3
YFGRAZUYIUBWJO-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
FO9 Binding MOAD:  6G3Q Ki: 57.9 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.01 Å
  • R-Value Free: 0.151 
  • R-Value Work: 0.127 
  • R-Value Observed: 0.128 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.316α = 90
b = 41.439β = 104.34
c = 72.112γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-28
    Type: Initial release