1IF9 | pdb_00001if9

Carbonic Anhydrase II Complexed With N-[2-(1H-Indol-5-yl)-butyl]-4-sulfamoyl-benzamide

• PDB DOI: https://doi.org/10.2210/pdb1IF9/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-04-12 Released: 2001-05-02 
• Deposition Author(s): Grzybowski, B.A., Ishchenko, A.V., Kim, C.-Y., Topalov, G., Chapman, R., Christianson, D.W., Whitesides, G.M., Shakhnovich, E.I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.216 (Depositor) 
• R-Value Work: 
  0.156 (Depositor) 

Starting Model: experimental

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

• PubMed: 11818565 
• DOI: https://doi.org/10.1073/pnas.032673399
• Primary Citation 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. 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.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 29.8 kDa 
• Atom Count: 2,285 
• Modeled Residue Count: 258 
• Deposited Residue Count: 259 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CARBONIC ANHYDRASE II	A	259	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
SBB	D [auth A]	N-[2-(1H-INDOL-5-YL)-BUTYL]-4-SULFAMOYL-BENZAMIDE C19 H21 N3 O3 S FSRPBGBMEKDSIJ-CYBMUJFWSA-N
HG	C [auth A]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.216 (Depositor) 
• R-Value Work:  0.156 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.3	α = 90
b = 40.8	β = 104.6
c = 72.4	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-05-02 
Deposition Author(s): Grzybowski, B.A., Ishchenko, A.V., Kim, C.-Y., Topalov, G., Chapman, R., Christianson, D.W., Whitesides, G.M., Shakhnovich, E.I.

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: 2018-04-04
  Changes: Data collection
• Version 1.4: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description