2FOV

Human Carbonic Anhydrase II complexed with two-prong inhibitors


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 

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This is version 1.2 of the entry. See complete history


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

  • 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 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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Carbonic Anhydrase IIA260Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00918
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B30
Query on B30

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

Download Ideal Coordinates CCD File 
C [auth A]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
CCN
Query on CCN

Download Ideal Coordinates CCD File 
F [auth A]ACETONITRILE
C2 H3 N
WEVYAHXRMPXWCK-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CMH
Query on CMH
A L-PEPTIDE LINKINGC4 H9 Hg N O2 SCYS
Binding Affinity Annotations 
IDSourceBinding 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 = 42.362α = 90
b = 41.482β = 104.34
c = 72.234γ = 90
Software Package:
Software NamePurpose
SHELXmodel building
SHELXL-97refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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