2HNC

Crystal structure of the human carbonic anhydrase II in complex with the 5-amino-1,3,4-thiadiazole-2-sulfonamide inhibitor.

• PDB DOI:  https://doi.org/10.2210/pdb2HNC/pdb

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


• Deposited: 2006-07-12 Released: 2006-12-19 
• Deposition Author(s): Menchise, V., Di Fiore, A., De Simone, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.215 
• R-Value Work: 0.194 

Literature

Carbonic anhydrase inhibitors: X-ray crystallographic studies for the binding of 5-amino-1,3,4-thiadiazole-2-sulfonamide and 5-(4-amino-3-chloro-5-fluorophenylsulfonamido)-1,3,4-thiadiazole-2-sulfonamide to human isoform II.

Menchise, V., De Simone, G., Di Fiore, A., Scozzafava, A., Supuran, C.T.

(2006) Bioorg Med Chem Lett 16: 6204-6208

• PubMed: 17000110 
• DOI: https://doi.org/10.1016/j.bmcl.2006.09.022
• Primary Citation of Related Structures:  
  2HNC, 2HOC


• PubMed Abstract: 
  

The X-ray crystal structures of 5-amino-1,3,4-thiadiazole-2-sulfonamide (the acetazolamide precursor) and 5-(4-amino-3-chloro-5-fluorophenylsulfonamido)-1,3,4-thiadiazole-2-sulfonamide in complex with the human isozyme II of carbonic anhydrase (CA, EC 4.2.1.1) are reported. The thiadiazole-sulfonamide moiety of the two compounds binds in the canonic manner to the zinc ion and interacts with Thr199, Glu106, and Thr200. The substituted phenyl tail of the second inhibitor was positioned in the hydrophobic part of the binding pocket, at van der Waals distance from Phe131, Val 135, Val141, Leu198, Pro202, and Leu204. These structures may help in the design of better inhibitors of these widespread zinc-containing enzymes.

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Related Citations: 

• Refined structure of human carbonic anhydrase II at 2.0 A resolution.
  Eriksson, A.E., Jones, T.A., Liljas, A.
  (1988) Proteins 4: 274

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Organizational Affiliation: 

Istituto di Biostrutture e Bioimmagini-CNR, via Mezzocannone 16, 80134 Naples, Italy.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 29.91 kDa 
• Atom Count: 2,280 
• Modelled Residue Count: 257 
• Deposited Residue Count: 259 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	259	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MBO	D [auth A]	MERCURIBENZOIC ACID C7 H5 Hg O2 FVFZSVRSDNUCGG-UHFFFAOYSA-N
1SA	C [auth A]	5-AMINO-1,3,4-THIADIAZOLE-2-SULFONAMIDE C2 H4 N4 O2 S2 VGMVBPQOACUDRU-UHFFFAOYSA-N
GOL	E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
1SA	Binding MOAD:  2HNC	Ki: 60 (nM) from 1 assay(s)
	BindingDB:  2HNC	Ki: min: 60, max: 6.00e+4 (nM) from 4 assay(s)
		IC50: min: 2750, max: 7400 (nM) from 6 assay(s)
	PDBBind:  2HNC	Ki: 60 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.215 
• R-Value Work: 0.194 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.11	α = 90
b = 41.31	β = 104.35
c = 71.89	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-19 
Deposition Author(s): Menchise, V., Di Fiore, A., De Simone, G.

Revision History  

• Version 1.0: 2006-12-19
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description