1JR1

Crystal structure of Inosine Monophosphate Dehydrogenase in complex with Mycophenolic Acid

• PDB DOI: https://doi.org/10.2210/pdb1JR1/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Cricetulus griseus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-08-09 Released: 2001-09-05 
• Deposition Author(s): Sintchak, M.D., Fleming, M.A., Futer, O., Raybuck, S.A., Chambers, S.P., Caron, P.R., Murcko, M.A., Wilson, K.P.

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Experimental Data Snapshot

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

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: 8681386 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

Vertex Pharmaceuticals Incorporated, Cambridge, Massachusetts 02139-4211, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inosine-5'-Monophosphate Dehydrogenase 2	A, B	514	Cricetulus griseus	Mutation(s): 0  EC: 1.1.1.205
UniProt
Find proteins for P12269 (Cricetulus griseus) Explore P12269  Go to UniProtKB:  P12269

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IMP	D [auth A], G [auth B]	INOSINIC ACID C10 H13 N4 O8 P GRSZFWQUAKGDAV-KQYNXXCUSA-N
MOA	E [auth A], H [auth B]	MYCOPHENOLIC ACID C17 H20 O6 HPNSFSBZBAHARI-RUDMXATFSA-N
K	C [auth A], F [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding 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 = 110.6	α = 90
b = 110.6	β = 90
c = 111	γ = 90

Software Package:

Software Name	Purpose
PHASES	phasing
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-09-05 
Deposition Author(s): Sintchak, M.D., Fleming, M.A., Futer, O., Raybuck, S.A., Chambers, S.P., Caron, P.R., Murcko, M.A., Wilson, K.P.

Revision History  

• 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