Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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: 95.30 kDa 
• Atom Count: 5888 
• Modelled Residue Count: 725 
• Deposited Residue Count: 828 
• Unique protein chains: 1

4I3L

Crystal structure of a metabolic reductase with 6-benzyl-1-hydroxy-4-methylpyridin-2(1H)-one

• PDB DOI: 10.2210/pdb4I3L/pdb

• Classification: oxidoreductase/oxidoreductase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-11-26 Released: 2013-05-22 
• Deposition Author(s): Zheng, B., Yao, Y., Liu, Z., Deng, L., Anglin, J.L., Jiang, H., Prasad, B.V.V., Song, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.29 Å
• R-Value Free: 0.293 
• R-Value Work: 0.220 
• R-Value Observed: 0.223 

Literature

Crystallographic Investigation and Selective Inhibition of Mutant Isocitrate Dehydrogenase.

Zheng, B., Yao, Y., Liu, Z., Deng, L., Anglin, J.L., Jiang, H., Prasad, B.V., Song, Y.

(2013) ACS Med Chem Lett 4: 542-546

• PubMed: 23795241 
• DOI: 10.1021/ml400036z
• Primary Citation of Related Structures:  
  4I3K, 4I3L


• PubMed Abstract: 
  

Mutations in isocitrate dehydrogenase (IDH), a key enzyme in the tricarboxylic acid cycle, have recently been found in ~75% glioma and ~20% acute myeloid leukemia. Different from the wild-type enzyme, mutant IDH1 catalyzes the reduction of α-ketoglutaric acid to D -2-hydroxyglutaric acid. Strong evidence has shown mutant IDH1 represents a novel target for this type of cancer. We found two 1-hydroxypyridin-2-one compounds that are potent inhibitors of R132H and R132C IDH1 mutants with K _i values as low as 120 nM. These compounds exhibit >60-fold selectivity against wild-type IDH1 and can inhibit the production of D -2-hydroxyglutaric acid in IDH1 mutated cells, representing novel chemical probes for cancer biology studies. We also report the first inhibitor-bound crystal structures of IDH1(R132H), showing these inhibitors have H-bond, electrostatic and hydrophobic interactions with the mutant enzyme. Comparison with the substrate-bound IDH1 structures revealed the structural basis for the high enzyme selectivity of these compounds.

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Organizational Affiliation: 

Department of Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isocitrate dehydrogenase [NADP] cytoplasmic	A, B	414	Homo sapiens	Mutation(s): 1  Gene Names: IDH1, PICD EC: 1.1.1.42
UniProt & NIH Common Fund Data Resources
Find proteins for O75874 (Homo sapiens) Explore O75874  Go to UniProtKB:  O75874
PHAROS:  O75874 GTEx:  ENSG00000138413

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	C [auth A], G [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
1BZ	F [auth A]	6-benzyl-1-hydroxy-4-methylpyridin-2(1H)-one C13 H13 N O2 AVLZAVSZOAQKRC-UHFFFAOYSA-N
SO4	D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
1BZ	BindingDB:  4I3L	Ki: min: 120, max: 5.00e+4 (nM) from 5 assay(s)
		IC50: min: 120, max: 3.00e+4 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.29 Å
• R-Value Free: 0.293 
• R-Value Work: 0.220 
• R-Value Observed: 0.223 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.853	α = 90
b = 80.853	β = 90
c = 304.836	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
PHASES	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-11-26 
• Released Date: 2013-05-22 
Deposition Author(s): Zheng, B., Yao, Y., Liu, Z., Deng, L., Anglin, J.L., Jiang, H., Prasad, B.V.V., Song, Y.

Revision History  

• Version 1.0: 2013-05-22
  Type: Initial release
  
• Version 1.1: 2013-07-10
  Changes: Database references