3K2F | pdb_00003k2f

Nitric oxide-donating carbonic anhydrase inhibitors for the treatment of open-angle glaucoma

• PDB DOI: https://doi.org/10.2210/pdb3K2F/pdb

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


• Deposited: 2009-09-30 Released: 2009-11-17 
• Deposition Author(s): Temperini, C., Cecchi, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 
  0.272 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

Nitric oxide-donating carbonic anhydrase inhibitors for the treatment of open-angle glaucoma

Steele, R.M., Benedini, F., Biondi, S., Borghi, V., Carzaniga, L., Impagnatiello, F., Miglietta, D., Chong, W.K., Rajapakse, R., Cecchi, A., Temperini, C., Supuran, C.T.

(2009) Bioorg Med Chem Lett 19: 6565-6570

• PubMed: 19854054 
• DOI: https://doi.org/10.1016/j.bmcl.2009.10.036
• Primary Citation Related Structures: 
  3K2F


• PubMed Abstract: 
  

  Novel bi-functional compounds with a nitric oxide (NO)-releasing moiety bound to a dorzolamide scaffold were investigated. Several compounds were synthesized and their activity as selective carbonic anhydrase inhibitors (CAI) evaluated in vitro on recombinant hCA type I, II and IV enzyme isoforms where they showed different degrees of potency and selectivity to hCA II. A high resolution X-ray crystal structure for the CA II adduct with 8 confirmed the high affinity of this class of compounds for the enzyme. Compounds 4, 6, and 8 showed highly potent and efficacious NO-mediated properties as assessed by their vascular relaxant effect on methoxamine-precontracted rabbit aortic rings. Finally, compounds 4 and 6 exerted potent intraocular pressure (IOP) lowering effects in vivo in normotensive rabbits thereby anticipating their potential for the treatment of hypertensive glaucoma.

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Organizational Affiliation: 
• NicOx Research Institute, 20091 Bresso, Milan, Italy. [e-mail]

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: 30.09 kDa 
• Atom Count: 2,194 
• Modeled 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	N/A	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
NKX	D [auth A]	(2S)-2,3-bis(nitrooxy)propyl ethyl[(4S,6S)-6-methyl-7,7-dioxido-2-sulfamoyl-5,6-dihydro-4H-thieno[2,3-b]thiopyran-4-yl]carbamate C14 H20 N4 O12 S3 RFISBOUXKIOATP-QXEWZRGKSA-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: 1.98 Å
• R-Value Free:  0.272 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.63	α = 90
b = 42.01	β = 104.4
c = 71.46	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: 2009-11-17 
Deposition Author(s): Temperini, C., Cecchi, A.

Revision History  

• Version 1.0: 2009-11-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description