Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 29.83 kDa 
• Atom Count: 2138 
• Modelled Residue Count: 257 
• Deposited Residue Count: 259 
• Unique protein chains: 1

1BNV

CARBONIC ANHYDRASE II INHIBITOR

• PDB DOI: 10.2210/pdb1BNV/pdb

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


• Deposited: 1998-07-30 Released: 1999-02-16 
• Deposition Author(s): Boriack-Sjodin, P.A., Zeitlin, S., Christianson, D.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Work: 0.139 
• R-Value Observed: 0.139 

Literature

Structural analysis of inhibitor binding to human carbonic anhydrase II.

Boriack-Sjodin, P.A., Zeitlin, S., Chen, H.H., Crenshaw, L., Gross, S., Dantanarayana, A., Delgado, P., May, J.A., Dean, T., Christianson, D.W.

(1998) Protein Sci 7: 2483-2489

• PubMed: 9865942 
• DOI: 10.1002/pro.5560071201
• Primary Citation of Related Structures:  
  1BN1, 1BN3, 1BN4, 1BNM, 1BNN, 1BNQ, 1BNT, 1BNU, 1BNV, 1BNW


• PubMed Abstract: 
  

X-ray crystal structures of carbonic anhydrase II (CAII) complexed with sulfonamide inhibitors illuminate the structural determinants of high affinity binding in the nanomolar regime. The primary binding interaction is the coordination of a primary sulfonamide group to the active site zinc ion. Secondary interactions fine-tune tight binding in regions of the active site cavity >5 A away from zinc, and this work highlights three such features: (1) advantageous conformational restraints of a bicyclic thienothiazene-6-sulfonamide-1,1-dioxide inhibitor skeleton in comparison with a monocyclic 2,5-thiophenedisulfonamide skeleton; (2) optimal substituents attached to a secondary sulfonamide group targeted to interact with hydrophobic patches defined by Phe131, Leu198, and Pro202; and (3) optimal stereochemistry and configuration at the C-4 position of bicyclic thienothiazene-6-sulfonamides; the C-4 substituent can interact with His64, the catalytic proton shuttle. Structure-activity relationships rationalize affinity trends observed during the development of brinzolamide (Azopt), the newest carbonic anhydrase inhibitor approved for the treatment of glaucoma.

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Organizational Affiliation: 

Department of Chemistry, University of Pennsylvania, Philadelphia 19104-6323, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CARBONIC ANHYDRASE	A	259	Homo sapiens	Mutation(s): 0  Gene Names: CA2 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
AL7	D [auth A]	(S)-3,4-DIHYDRO-2-(3-METHOXYPHENYL)-4-METHYLAMINO-2H-THIENO[3,2-E]-1,2-THIAZINE-6-SULFONAMIDE-1,1-DIOXIDE C14 H17 N3 O5 S3 RMOXCYSVWCHXII-GFCCVEGCSA-N
HG	B [auth A]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
AL7	PDBBind:  1BNV	Kd: 1.7 (nM) from 1 assay(s)
	Binding MOAD:  1BNV	Kd: 1.7 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Work: 0.139 
• R-Value Observed: 0.139 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.7	α = 90
b = 41.7	β = 104.6
c = 73	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
MOSFLM	data reduction
CCP4	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-07-30 
• Released Date: 1999-02-16 
Deposition Author(s): Boriack-Sjodin, P.A., Zeitlin, S., Christianson, D.W.

Revision History  

• Version 1.0: 1999-02-16
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance