2X7U

Structures of human carbonic anhydrase II inhibitor complexes reveal a second binding site for steroidal and non-steroidal inhibitors.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of Human Carbonic Anhydrase II/Inhibitor Complexes Reveal a Second Binding Site for Steroidal and Non-Steroidal Inhibitors.

Cozier, G.E.Leese, M.P.Lloyd, M.D.Baker, M.D.Thiyagarajan, N.Acharya, K.R.Potter, B.V.L.

(2010) Biochemistry 49: 3464

  • DOI: 10.1021/bi902178w
  • Primary Citation of Related Structures:  
  • Also Cited By: 3OKV, 3OKU, 3OIM, 3OIL, 3OIK

  • PubMed Abstract: 
  • Carbonic anhydrase (CA) catalyzes the reversible hydration of carbon dioxide to hydrogen carbonate, and its role in maintaining pH balance has made it an attractive drug target. Steroidal sulfamate esters, inhibitors of the cancer drug target steroid ...

    Carbonic anhydrase (CA) catalyzes the reversible hydration of carbon dioxide to hydrogen carbonate, and its role in maintaining pH balance has made it an attractive drug target. Steroidal sulfamate esters, inhibitors of the cancer drug target steroid sulfatase (STS), are sequestered in vivo by CA II in red blood cells, which may be the origin of their excellent drug properties. Understanding the structural basis of this is important for drug design. Structures of CA II complexed with 2-methoxyestradiol 3-O-sulfamate (3), 2-ethylestradiol 3,17-O,O-bis(sulfamate) (4), and 2-methoxyestradiol 17-O-sulfamate (5) are reported to 2.10, 1.85, and 1.64 A, respectively. Inhibitor 3 interacts with the active site Zn(II) ion through the 3-O-sulfamate, while inhibitors 4 and 5 bind through their 17-O-sulfamate. Comparison of the IC(50) values for CA II inhibition gave respective values of 56, 662, 2113, 169, 770, and 86 nM for estrone 3-O-sulfamate (1), 2-methoxyestradiol 3,17-O,O-bis(sulfamate) (2), 3, 4, 5, and 5'-((4H-1,2,4-triazol-4-yl)methyl)-3-chloro-2'-cyanobiphenyl-4-yl sulfamate (6), a nonsteroidal dual aromatase-sulfatase inhibitor. Inhibitors 2, 5, and 6 showed binding to a second adjacent site that is capable of binding both steroidal and nonsteroidal ligands. Examination of both IC(50) values and crystal structures suggests that 2-substituents on the steroid nucleus hinder binding via a 3-O-sulfamate, leading to coordination through a 17-O-sulfamate if present. These results underline the influence of small structural changes on affinity and mode of binding, the degree of flexibility in the design of sulfamate-based inhibitors, and suggest a strategy for inhibitors which interact with both the active site and the second adjacent binding site simultaneously that could be both potent and selective.


    Organizational Affiliation

    Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath,Claverton Down, Bath BA2 7AY, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CARBONIC ANHYDRASE 2
A
259Homo 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
ZN
Query on ZN

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

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Download CCD File 
A
(9BETA,14BETA,17BETA)-17-HYDROXY-2-METHOXYESTRA-1,3,5(10)-TRIEN-3-YL SULFAMATE
C19 H27 N O5 S
RWIXFHUXVURZCZ-SSTWWWIQSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
WZAKi: 5340 nM BINDINGMOAD
WZAKi: 5340 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 42.502α = 90.00
b = 69.540β = 90.00
c = 73.207γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
PHASERphasing
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-03-31
    Type: Initial release
  • Version 1.1: 2011-05-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance