1IF7

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.214 

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
  • Primary Citation of Related Structures:  
    1IF7, 1IF8, 1IF9

  • 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 conformations ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CARBONIC ANHYDRASE IIA259Homo 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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SBR (Subject of Investigation/LOI)
Query on SBR

Download Ideal Coordinates CCD File 
D [auth A](R)-N-(3-INDOL-1-YL-2-METHYL-PROPYL)-4-SULFAMOYL-BENZAMIDE
C19 H21 N3 O3 S
ZFWHOUCRVSOZJE-CQSZACIVSA-N
 Ligand Interaction
HG
Query on HG

Download Ideal Coordinates CCD File 
C [auth A]MERCURY (II) ION
Hg
BQPIGGFYSBELGY-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
SBR PDBBind:  1IF7 Kd: 0.03 (nM) from 1 assay(s)
Binding MOAD:  1IF7 Kd: 0.03 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.214 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.8α = 90
b = 41.8β = 104.7
c = 73.4γ = 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  (Full details and data files)

  • 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