3NI5

Carbonic anhydrase inhibitor: C1 family

• PDB DOI: https://doi.org/10.2210/pdb3NI5/pdb

• Classification: Lyase/Lyase INHIBITOR
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2010-06-15 Released: 2011-06-22 
• Deposition Author(s): Temperini, C., Cecchi, A., Scozzafava, A., Supuran, C.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.272 
• R-Value Work: 0.229 
• R-Value Observed: 0.231 

Starting Model: experimental

Literature

Synthesis and crystallographic analysis of new sulfonamides incorporating NO-donating moieties with potent antiglaucoma action

Mincione, F., Benedini, F., Biondi, S., Cecchi, A., Temperini, C., Formicola, G., Pacileo, I., Scozzafava, A., Masini, E., Supuran, C.T.

(2011) Bioorg Med Chem Lett 21: 3216-3221

• PubMed: 21549597 
• DOI: https://doi.org/10.1016/j.bmcl.2011.04.046
• Primary Citation of Related Structures:  
  3NI5


• PubMed Abstract: 
  

  Several aromatic/heterocyclic sulfonamide scaffolds have been used to synthesize compounds incorporating NO-donating moieties of the nitrate ester type, which have been investigated for the inhibition of five physiologically relevant human carbonic anhydrase (hCA, EC 4.2.1.1) isoforms: hCA I (offtarget), II, IV and XII (antiglaucoma targets) and IX (antitumor target). Some of the new compounds showed effective in vitro inhibition of the target isoforms involved in glaucoma, and the X-ray crystal structure of one of them revealed factors associated with the marked inhibitory activity. In an animal model of ocular hypertension, one of the new compounds was twice more effective than dorzolamide in reducing elevated intraocular pressure characteristic of this disease, anticipating their potential for the treatment of glaucoma.

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Organizational Affiliation: 

U.O. Oculistica Az. USL 3, Val di Nievole, Ospedale di Pescia, Pescia, 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: 30.04 kDa 
• Atom Count: 2,202 
• 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
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
C1H	D [auth A]	4-(nitrooxy)butyl 3-[(5-sulfamoyl-1,3,4-thiadiazol-2-yl)sulfamoyl]benzoate C13 H15 N5 O9 S3 QCXYDHYYUCXOLH-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
C1H	BindingDB:  3NI5	Ki: 28 (nM) from 1 assay(s)
	PDBBind:  3NI5	Ki: 28 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.272 
• R-Value Work: 0.229 
• R-Value Observed: 0.231 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.79	α = 90
b = 42.11	β = 104.4
c = 72.02	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-22 
Deposition Author(s): Temperini, C., Cecchi, A., Scozzafava, A., Supuran, C.T.

Revision History  

• Version 1.0: 2011-06-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description