3OY0 | pdb_00003oy0

Human Carbonic Anhydrase II complexed with 1-(4-(4-(2-(ISOPROPYLSULFONYL)PHENYLAMINO)-1H-PYRROLO[2,3-B]PYRIDIN-6-YLAMINO)-3-METHOXYPHENYL)PIPERIDIN-4-OL

• PDB DOI: https://doi.org/10.2210/pdb3OY0/pdb

• Classification: lyase/lyase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-09-22 Released: 2011-08-10 
• Deposition Author(s): Aggarwal, M., McKenna, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.192 (Depositor), 0.184 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.157 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

Anticonvulsant 4-aminobenzenesulfonamide derivatives with branched-alkylamide moieties: X-ray crystallography and inhibition studies of human carbonic anhydrase isoforms I, II, VII, and XIV.

Hen, N., Bialer, M., Yagen, B., Maresca, A., Aggarwal, M., Robbins, A.H., McKenna, R., Scozzafava, A., Supuran, C.T.

(2011) J Med Chem 54: 3977-3981

• PubMed: 21506569 
• DOI: https://doi.org/10.1021/jm200209n
• Primary Citation Related Structures: 
  3OY0, 3OYQ, 3OYS


• PubMed Abstract: 
  

  Aromatic amides comprising branched aliphatic carboxylic acids and 4-aminobenzenesulfonamide were evaluated for their inhibition of carbonic anhydrase (CA) isoforms. Of the most anticonvulsant-active compounds (2, 4, 13, 16, and 17), only 13, 16, and 17 were potent inhibitors of CAs VII and XIV. Compounds 9, 14, and 19 inhibited CA II, while 10 and 12 inhibited all isoforms. Structural studies suggest that differences in the active sites' hydrophobicity modulate the affinity of the inhibitors.

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Organizational Affiliation: 
• Institute for Drug Research, The Hebrew University of Jerusalem , Jerusalem, Israel.

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: 29.84 kDa 
• Atom Count: 2,305 
• Modeled Residue Count: 257 
• 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 GTEx:  ENSG00000104267

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OY0	C [auth A]	(2S)-2-tert-butyl-N-(4-sulfamoylphenyl)pentanamide C15 H24 N2 O3 S WYSWMHFXVFMYFI-CYBMUJFWSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	E [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
OY0	BindingDB:  3OY0	Ki: 10.1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.192 (Depositor), 0.184 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.157 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.235	α = 90
b = 41.331	β = 104.15
c = 72.028	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-10 
Deposition Author(s): Aggarwal, M., McKenna, R.

Revision History  

• Version 1.0: 2011-08-10
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description