1JR1 | pdb_00001jr1

Crystal structure of Inosine Monophosphate Dehydrogenase in complex with Mycophenolic Acid

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.285 (Depositor) 
  • R-Value Work: 
    0.217 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history. 

Literature

Structure and mechanism of inosine monophosphate dehydrogenase in complex with the immunosuppressant mycophenolic acid.

Sintchak, M.D., Fleming, M.A., Futer, O., Raybuck, S.A., Chambers, S.P., Caron, P.R., Murcko, M.A., Wilson, K.P.

(1996) Cell 85: 921-930

  • DOI: https://doi.org/10.1016/s0092-8674(00)81275-1
  • Primary Citation Related Structures: 
    1JR1

  • PubMed Abstract: 

    The structure of inosine-5'-monophosphate dehydrogenase (IMPDH) in complex with IMP and mycophenolic acid (MPA) has been determined by X-ray diffraction. IMPDH plays a central role in B and T lymphocyte replication. MPA is a potent IMPDH inhibitor and the active metabolite of an immunosuppressive drug recently approved for the treatment of allograft rejection. IMPDH comprises two domains: a core domain, which is an alpha/beta barrel and contains the active site, and a flanking domain. The complex, in combination with mutagenesis and kinetic data, provides a structural basis for understanding the mechanism of IMPDH activity and indicates that MPA inhibits IMPDH by acting as a replacement for the nicotinamide portion of the nicotinamide adenine dinucleotide cofactor and a catalytic water molecule.

    • Organizational Affiliation: 
    • Vertex Pharmaceuticals Incorporated, Cambridge, Massachusetts 02139-4211, USA.

Macromolecule Content 

  • Total Structure Weight: 113.34 kDa 
  • Atom Count: 6,296 
  • Modeled Residue Count: 804 
  • Deposited Residue Count: 1,028 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Inosine-5'-Monophosphate Dehydrogenase 2
A, B
514Cricetulus griseusMutation(s): 0 
EC: 1.1.1.205
UniProt
Find proteins for P12269 (Cricetulus griseus)
Explore P12269 
Go to UniProtKB:  P12269
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12269
Sequence Annotations
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Reference Sequence

Small Molecules

Binding Affinity Annotations 
IDSourceBinding Affinity
MOA BindingDB:  1JR1 Ki: min: 6, max: 10 (nM) from 3 assay(s)
IC50: min: 11, max: 2.00e+4 (nM) from 13 assay(s)
EC50: 540 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.285 (Depositor) 
  • R-Value Work:  0.217 (Depositor) 
Space Group: P 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.6α = 90
b = 110.6β = 90
c = 111γ = 90
Software Package:
Software NamePurpose
PHASESphasing
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-09-05
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary