1JR1

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 
  • R-Value Work: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: 10.1016/s0092-8674(00)81275-1
  • Primary Citation of 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Inosine-5'-Monophosphate Dehydrogenase 2A, B514Cricetulus griseusMutation(s): 0 
Gene Names: IMPDH2
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IMP
Query on IMP

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
INOSINIC ACID
C10 H13 N4 O8 P
GRSZFWQUAKGDAV-KQYNXXCUSA-N
 Ligand Interaction
MOA
Query on MOA

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
MYCOPHENOLIC ACID
C17 H20 O6
HPNSFSBZBAHARI-RUDMXATFSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
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)
PDBBind:  1JR1 Ki: 6 (nM) from 1 assay(s)
IMP BindingDB:  1JR1 Ki: 250 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

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

View Full Validation Report



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