3BL1 | pdb_00003bl1

Carbonic anhydrase inhibitors. Sulfonamide diuretics revisited old leads for new applications

• PDB DOI: https://doi.org/10.2210/pdb3BL1/pdb

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


• Deposited: 2007-12-10 Released: 2008-07-01 
• Deposition Author(s): Temperini, C., Cecchi, A., Supuran, C.T.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.299 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Literature

Carbonic anhydrase inhibitors. Interaction of indapamide and related diuretics with 12 mammalian isozymes and X-ray crystallographic studies for the indapamide-isozyme II adduct.

Temperini, C., Cecchi, A., Scozzafava, A., Supuran, C.T.

(2008) Bioorg Med Chem Lett 18: 2567-2573

• PubMed: 18374572 
• DOI: https://doi.org/10.1016/j.bmcl.2008.03.051
• Primary Citation of Related Structures:  
  3BL1


• PubMed Abstract: 
  

  Diuretics such as hydrochlorothiazide, hydroflumethiazide, quinethazone, metolazone, chlorthalidone, indapamide, furosemide, and bumetanide containing primary sulfamoyl moieties were reevaluated as inhibitors of 12 human carbonic anhydrases (hCAs, EC 4.2.1.1). These drugs considerably inhibit (low nanomolar range) some CA isozymes involved in critical physiologic processes, among the 16 present in vertebrates, for example, metolazone against CA VII, XII, and XIII, chlorthalidone against CA VB, VII, IX, XII, and XIII, indapamide against CA VII, IX, XII, and XIII, furosemide against CA I, II, and XIV, and bumetanide against CA IX and XII. The X-ray crystal structure of the hCA II-indapamide adduct was also resolved at high resolution.

---

Organizational Affiliation: 

Università degli Studi di Firenze, Laboratorio di Chimica Bioinorganica, Room 188, Via della Lastruccia 3, I-50019 Sesto Fiorentino (Firenze), Italy.

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: 29.92 kDa 
• Atom Count: 2,231 
• 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  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
BL1	D [auth A]	4-chloro-N-[(2S)-2-methyl-2,3-dihydro-1H-indol-1-yl]-3-sulfamoylbenzamide C16 H16 Cl N3 O3 S NDDAHWYSQHTHNT-JTQLQIEISA-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: 2.10 Å
• R-Value Free:  0.299 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.05	α = 90
b = 41.32	β = 104.29
c = 72.25	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: 2008-07-01 
Deposition Author(s): Temperini, C., Cecchi, A., Supuran, C.T.

Revision History  

• Version 1.0: 2008-07-01
  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, Source and taxonomy
• Version 1.4: 2024-02-21
  Changes: Data collection, Database references, Derived calculations