1IF8

Carbonic Anhydrase II Complexed With (S)-N-(3-Indol-1-yl-2-methyl-propyl)-4-sulfamoyl-benzamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Combinatorial computational method gives new picomolar ligands for a known enzyme.

Grzybowski, B.A.Ishchenko, A.V.Kim, C.Y.Topalov, G.Chapman, R.Christianson, D.W.Whitesides, G.M.Shakhnovich, E.I.

(2002) Proc Natl Acad Sci U S A 99: 1270-1273

  • DOI: 10.1073/pnas.032673399
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Combinatorial small molecule growth algorithm was used to design inhibitors for human carbonic anhydrase II. Two enantiomeric candidate molecules were predicted to bind with high potency (with R isomer binding stronger than S), but in two distinct co ...

    Combinatorial small molecule growth algorithm was used to design inhibitors for human carbonic anhydrase II. Two enantiomeric candidate molecules were predicted to bind with high potency (with R isomer binding stronger than S), but in two distinct conformations. The experiments verified that computational predictions concerning the binding affinities and the binding modes were correct for both isomers. The designed R isomer is the best-known inhibitor (K(d) approximately 30 pM) of human carbonic anhydrase II.


    Organizational Affiliation

    Harvard University, Department of Chemistry and Chemical Biology, 12 Oxford Street, Cambridge, MA 02138, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CARBONIC ANHYDRASE II
A
259Homo sapiensMutation(s): 0 
Gene Names: CA2
EC: 4.2.1.1
Find proteins for P00918 (Homo sapiens)
Go to UniProtKB:  P00918
NIH Common Fund Data Resources
PHAROS  P00918
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SBS
Query on SBS

Download CCD File 
A
(S)-N-(3-INDOL-1-YL-2-METHYL-PROPYL)-4-SULFAMOYL-BENZAMIDE
C19 H21 N3 O3 S
ZFWHOUCRVSOZJE-AWEZNQCLSA-N
 Ligand Interaction
HG
Query on HG

Download CCD File 
A
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SBSKd :  0.23000000417232513   nM  PDBBind
SBSKd:  0.23000000417232513   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.2α = 90
b = 42.3β = 104.7
c = 73.9γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-05-02
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Data collection
  • Version 1.4: 2018-04-04
    Changes: Data collection