3B4F

Carbonic anhydrase inhibitors. Interaction of 2-(hydrazinocarbonyl)-3-phenyl-1H-indole-5-sulfonamide with twelve mammalian isoforms: kinetic and X-Ray crystallographic studies

• PDB DOI:  https://doi.org/10.2210/pdb3B4F/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2007-10-24 Released: 2008-01-22 
• Deposition Author(s): Guzel, o., Temperini, c., Innocenti, a., Scozzafava, A., Salman, a., Supuran, c.t.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.239 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 

Literature

Carbonic anhydrase inhibitors. Interaction of 2-(hydrazinocarbonyl)-3-phenyl-1H-indole-5-sulfonamide with 12 mammalian isoforms: kinetic and X-ray crystallographic studies.

Guzel, O., Temperini, C., Innocenti, A., Scozzafava, A., Salman, A., Supuran, C.T.

(2008) Bioorg Med Chem Lett 18: 152-158

• PubMed: 18024029 
• DOI: https://doi.org/10.1016/j.bmcl.2007.10.110
• Primary Citation of Related Structures:  
  3B4F


• PubMed Abstract: 
  

2-(Hydrazinocarbonyl)-3-phenyl-1H-indole-5-sulfonamide was tested for its interaction with 12 carbonic anhydrase (CA, EC 4.2.1.1) isoforms in the search of compounds with good inhibitory activity against isozymes with medicinal chemistry applications, such as CA I, II, VA, VB, VII, IX, and XII among others. This sulfonamide is a potent inhibitor of CA I and II (K(I)s of 7.2-7.5 nM), a medium potency inhibitor of CA VII, IX, XII, and XIV, and a weak inhibitor against the other ubiquitous isoforms, making it thus a very interesting clinical candidate for situations in which a strong inhibition of CA I and II is needed. The crystal structure of the hCA II adduct of this sulfonamide revealed many favorable interactions between the inhibitor and the enzyme which explain its strong low nanomolar affinity for this isoform but may also be exploited for the design of effective inhibitors incorporating bicyclic moieties.

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Organizational Affiliation: 

Istanbul University, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, 34116 Beyazit, Istanbul, Turkey.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 29.89 kDa 
• Atom Count: 2,281 
• Modelled Residue Count: 256 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	260	Homo sapiens	Mutation(s): 0  Gene Names: CA2 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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TUO	D [auth A]	2-(hydrazinocarbonyl)-3-phenyl-1H-indole-5-sulfonamide C15 H14 N4 O3 S PPDLAUCFAOODER-UHFFFAOYSA-N
HG	C [auth A]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
TUO	Binding MOAD:  3B4F	Ki: 7.2 (nM) from 1 assay(s)
	BindingDB:  3B4F	Ki: 7.2 (nM) from 1 assay(s)
	PDBBind:  3B4F	Ki: 7.2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.239 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42	α = 90
b = 41.35	β = 104.35
c = 72.34	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrysalisPro	data collection
CrysalisPro	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-01-22 
Deposition Author(s): Guzel, o., Temperini, c., Innocenti, a., Scozzafava, A., Salman, a., Supuran, c.t.

Revision History  

• Version 1.0: 2008-01-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2018-04-04
  Changes: Data collection
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description