1JR1

Crystal structure of Inosine Monophosphate Dehydrogenase in complex with Mycophenolic Acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 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


  • 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 an ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Inosine-5'-Monophosphate Dehydrogenase 2
A, B
514Cricetulus griseusGene Names: IMPDH2
EC: 1.1.1.205
Find proteins for P12269 (Cricetulus griseus)
Go to Gene View: IMPDH2
Go to UniProtKB:  P12269
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
IMP
Query on IMP

Download SDF File 
Download CCD File 
A, B
INOSINIC ACID
C10 H13 N4 O8 P
GRSZFWQUAKGDAV-KQYNXXCUSA-N
 Ligand Interaction
MOA
Query on MOA

Download SDF File 
Download CCD File 
A, B
MYCOPHENOLIC ACID
6-(1,3-DIHYDRO-7-HYDROXY-5-METHOXY-4-METHYL-1-OXOISOBENZOFURAN-6-YL)-4-METHYL-4-HEXANOIC ACID
C17 H20 O6
HPNSFSBZBAHARI-RUDMXATFSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MOAEC50: 540 nM (98) BINDINGDB
MOAKi: 6 - 10 nM (98) BINDINGDB
MOAIC50: 11 - 1500 nM (98) BINDINGDB
MOAKi: 6 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.217 
  • Space Group: P 4
Unit Cell:
Length (Å)Angle (°)
a = 110.600α = 90.00
b = 110.600β = 90.00
c = 111.000γ = 90.00
Software Package:
Software NamePurpose
PHASESphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-09-05
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description