Biological Assembly 1  

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

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 29.60 kDa 
• Atom Count: 2246 
• Modelled Residue Count: 258 
• Deposited Residue Count: 259 
• Unique protein chains: 1

1TTM

Human carbonic anhydrase II complexed with 667-coumate

• PDB DOI: 10.2210/pdb1TTM/pdb

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


• Deposited: 2004-06-23 Released: 2004-10-05 
• Deposition Author(s): Lloyd, M.D., Pederick, R.L., Natesh, R., Woo, L.W.L., Purohit, A., Reed, M.J., Acharya, K.R., Potter, B.V.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.210 
• R-Value Work: 0.180 
• R-Value Observed: 0.180 

Literature

Crystal structure of human carbonic anhydrase II at 1.95 A resolution in complex with 667-coumate, a novel anti-cancer agent

Lloyd, M.D., Pederick, R.L., Natesh, R., Woo, L.W.L., Purohit, A., Reed, M.J., Acharya, K.R., Potter, B.V.L.

(2005) Biochem J 385: 715-720

• PubMed: 15453828 
• DOI: 10.1042/BJ20041037
• Primary Citation of Related Structures:  
  1TTM


• PubMed Abstract: 
  

CA (carbonic anhydrase) catalyses the reversible hydration of carbon dioxide into bicarbonate, and at least 14 isoforms have been identified in vertebrates. The role of CA type II in maintaining the fluid and pH balance has made it an attractive drug target for the treatment of glaucoma and cancer. 667-coumate is a potent inhibitor of the novel oncology target steroid sulphatase and is currently in Phase 1 clinical trials for hormone-dependent breast cancer. It also inhibits CA II in vitro. In the present study, CA II was crystallized with 667-coumate and the structure was determined by X-ray crystallography at 1.95 A (1 A=0.1 nm) resolution. The structure reported here is the first for an inhibitor based on a coumarin ring and shows ligation of the sulphamate group to the active-site zinc at 2.15 A through a nitrogen anion. The first two rings of the coumarin moiety are bound within the hydrophobic binding site of CA II. Important residues contributing to binding include Val-121, Phe-131, Val-135, Leu-141, Leu-198 and Pro-202. The third seven-membered ring is more mobile and is located in the channel leading to the surface of the enzyme. Pharmacokinetic studies show enhanced stability of 667-coumate in vivo and this has been ascribed to binding of CA II in erythrocytes. This result provides a structural basis for the stabilization and long half-life of 667-coumate in blood compared with its rapid disappearance in plasma, and suggests that reversible binding of inhibitors to CA may be a general method of delivering this type of labile drug.

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Organizational Affiliation: 

Medicinal Chemistry, Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase II	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
667	D [auth A]	6-OXO-8,9,10,11-TETRAHYDRO-7H-CYCLOHEPTA[C][1]BENZOPYRAN-3-O-SULFAMATE C14 H15 N O5 S DSLPMJSGSBLWRE-UHFFFAOYSA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
667	BindingDB:  1TTM	Ki: 21 (nM) from 1 assay(s)
		Kd: 45 (nM) from 1 assay(s)
		IC50: min: 17, max: 25 (nM) from 3 assay(s)
	PDBBind:  1TTM	Kd: 45 (nM) from 1 assay(s)
	Binding MOAD:  1TTM	Kd: 45 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.210 
• R-Value Work: 0.180 
• R-Value Observed: 0.180 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.525	α = 90
b = 72.522	β = 90
c = 75.379	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-06-23 
• Released Date: 2004-10-05 
Deposition Author(s): Lloyd, M.D., Pederick, R.L., Natesh, R., Woo, L.W.L., Purohit, A., Reed, M.J., Acharya, K.R., Potter, B.V.L.

Revision History  

• Version 1.0: 2004-10-05
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance