Biological Assembly 1  

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 98234.52 
• Atom Count: 6252 
• Residue Count: 850 
• Unique protein chains: 1

4UMY

IDH1 R132H in complex with cpd 1

• DOI: 10.2210/pdb4UMY/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): 1 


• Deposited: 2014-05-22 Released: 2014-11-19 
• Deposition Author(s): McLean, L., Zhang, Y., Mathieu, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.224 
• R-Value Work: 0.200 

Literature

Selective Inhibition of Mutant Isocitrate Dehydrogenase 1 (Idh1) Via Disruption of a Metal Binding Network by an Allosteric Small Molecule.

Deng, G., Shen, J., Yin, M., Mcmanus, J., Mathieu, M., Gee, P., He, T., Shi, C., Bedel, O., Mclean, L.R., Le-Strat, F., Zhang, Y., Marquette, J., Gao, Q., Zhang, B., Rak, A., Hoffmann, D., Rooney, E., Vassort, A., Englaro, W., Li, Y., Patel, V., Adrian, F., Gross, S., Wiederschain, D., Cheng, H., Licht, S.

(2015) J.Biol.Chem. 290: 762

• PubMed: 25391653 
• DOI: 10.1074/jbc.M114.608497
• Primary Citation of Related Structures:  
  4UMX


• PubMed Abstract: 
  

Cancer-associated point mutations in isocitrate dehydrogenase 1 and 2 (IDH1 and IDH2) confer a neomorphic enzymatic activity: the reduction of α-ketoglutarate to d-2-hydroxyglutaric acid, which is proposed to act as an oncogenic metabolite by inducing hypermethylation of histones and DNA. Although selective inhibitors of mutant IDH1 and IDH2 have been identified and are currently under investigation as potential cancer therapeutics, the mechanistic basis for their selectivity is not yet well understood. A high throughput screen for selective inhibitors of IDH1 bearing the oncogenic mutation R132H identified compound 1, a bis-imidazole phenol that inhibits d-2-hydroxyglutaric acid production in cells. We investigated the mode of inhibition of compound 1 and a previously published IDH1 mutant inhibitor with a different chemical scaffold. Steady-state kinetics and biophysical studies show that both of these compounds selectively inhibit mutant IDH1 by binding to an allosteric site and that inhibition is competitive with respect to Mg(2+). A crystal structure of compound 1 complexed with R132H IDH1 indicates that the inhibitor binds at the dimer interface and makes direct contact with a residue involved in binding of the catalytically essential divalent cation. These results show that targeting a divalent cation binding residue can enable selective inhibition of mutant IDH1 and suggest that differences in magnesium binding between wild-type and mutant enzymes may contribute to the inhibitors' selectivity for the mutant enzyme.

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Organizational Affiliation: 

From Division of Oncology Drug Discovery and Preclinical Development, Sanofi, Cambridge, Massachusetts 02139, [e-mail].

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
ISOCITRATE DEHYDROGENASE [NADP] CYTOPLASMIC	A, B	425	Homo sapiens	Mutation(s): 1  Gene Names: IDH1 (PICD) EC: 1.1.1.42
Find proteins for O75874 (Homo sapiens) Go to Gene View: IDH1 Go to UniProtKB:  O75874

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NAP	A, B	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.224 
• R-Value Work: 0.200 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 82.680	α = 90.00
b = 82.680	β = 90.00
c = 300.370	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data reduction
CNX	phasing
SCALEPACK	data scaling
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-05-22 
• Released Date: 2014-11-19 
• Deposition Author(s): McLean, L., Zhang, Y., Mathieu, M.

Revision History 

• Version 1.0: 2014-11-19
  Type: Initial release
• Version 1.1: 2014-11-26
  Type: Database references
• Version 1.2: 2015-01-21
  Type: Database references
• Version 1.3: 2017-03-29
  Type: Other