Biological Assembly 1  

 3D View: Structure | 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: 30.52 kDa 
• Atom Count: 2440 
• Modelled Residue Count: 259 
• Deposited Residue Count: 260 
• Unique protein chains: 1

2FOV

Human Carbonic Anhydrase II complexed with two-prong inhibitors

• DOI: 10.2210/pdb2FOV/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-01-14 Released: 2006-04-04 
• Deposition Author(s): Jude, K.M., Christianson, D.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 0.187 
• R-Value Work: 0.143 
• R-Value Observed: 0.143 

Literature

Ultrahigh resolution crystal structures of human carbonic anhydrases I and II complexed with two-prong inhibitors reveal the molecular basis of high affinity.

Jude, K.M., Banerjee, A.L., Haldar, M.K., Manokaran, S., Roy, B., Mallik, S., Srivastava, D.K., Christianson, D.W.

(2006) J Am Chem Soc 128: 3011-3018

• PubMed: 16506782 
• DOI: 10.1021/ja057257n
• Primary Citation of Related Structures:  
  2FOQ, 2FOS, 2FOU, 2FOV, 2FOY


• PubMed Abstract: 
  

The atomic-resolution crystal structures of human carbonic anhydrases I and II complexed with "two-prong" inhibitors are reported. Each inhibitor contains a benzenesulfonamide prong and a cupric iminodiacetate (IDA-Cu(2+)) prong separated by linkers of different lengths and compositions. The ionized NH(-) group of each benzenesulfonamide coordinates to the active site Zn(2+) ion; the IDA-Cu(2+) prong of the tightest-binding inhibitor, BR30, binds to H64 of CAII and H200 of CAI. This work provides the first evidence verifying the structural basis of nanomolar affinity measured for two-prong inhibitors targeting the carbonic anhydrases.

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Organizational Affiliation: 

Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic Anhydrase II	A	260	Homo sapiens	Mutation(s): 1  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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B30 (Subject of Investigation/LOI)	D [auth A], E [auth A]	{2,2'-[(2-{[4-(AMINOSULFONYL)BENZOYL]AMINO}ETHYL)IMINO]DIACETATO(2-)-KAPPAO}COPPER C13 H15 Cu N3 O7 S IZSCVVCMRVDVFM-UHFFFAOYSA-L
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU	C [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
CCN	F [auth A]	ACETONITRILE C2 H3 N WEVYAHXRMPXWCK-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CMH	A	L-PEPTIDE LINKING	C4 H9 Hg N O2 S		CYS

Binding Affinity Annotations
ID	Source	Binding Affinity
B30	Binding MOAD:  2FOV	Kd: 28 (nM) from 1 assay(s)
	PDBBind:  2FOV	Kd: 28 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 0.187 
• R-Value Work: 0.143 
• R-Value Observed: 0.143 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.362	α = 90
b = 41.482	β = 104.34
c = 72.234	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2006-01-14 
• Released Date: 2006-04-04 
Deposition Author(s): Jude, K.M., Christianson, D.W.

Revision History  

• Version 1.0: 2006-04-04
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance