Biological Assembly 1  

 3D View: Structure | Electron Density | 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: 95.54 kDa 
• Atom Count: 6211 
• Residue Count: 764 
• Unique protein chains: 1

4XS3

Crystal structure of a metabolic reductase with (E)-1-benzyl-5-((1-methyl-5-oxo-2-thioxoimidazolidin-4-ylidene)methyl)pyridin-2(1H)-one

• DOI: 10.2210/pdb4XS3/pdb

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


• Deposited: 2015-01-21 Released: 2016-07-27 
• Deposition Author(s): Zheng, B., Wu, F., Jiang, H., Kogiso, M., Yao, Y., Zhou, C., Li, X., Song, Y.
• Funding Organization(s): Cancer Prevention and Research Institute of Texas (CPRIT), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.29 Å
• R-Value Free: 0.283 
• R-Value Work: 0.226 
• R-Value Observed: 0.229 

Literature

Inhibition of Cancer-Associated Mutant Isocitrate Dehydrogenases by 2-Thiohydantoin Compounds.

Wu, F., Jiang, H., Zheng, B., Kogiso, M., Yao, Y., Zhou, C., Li, X.N., Song, Y.

(2015) J Med Chem 58: 6899-6908

• PubMed: 26280302 
• DOI: 10.1021/acs.jmedchem.5b00684
• Primary Citation of Related Structures:  
  4XRX, 4XS3


• PubMed Abstract: 
  

Somatic mutations of isocitrate dehydrogenase 1 (IDH1) at R132 are frequently found in certain cancers such as glioma. With losing the activity of wild-type IDH1, the R132H and R132C mutant proteins can reduce α-ketoglutaric acid (α-KG) to d-2-hydroxyglutaric acid (D2HG). The resulting high concentration of D2HG inhibits many α-KG-dependent dioxygenases, including histone demethylases, to cause broad histone hypermethylation. These aberrant epigenetic changes are responsible for the initiation of these cancers. We report the synthesis, structure-activity relationships, enzyme kinetics, and binding thermodynamics of a novel series of 2-thiohydantoin and related compounds, among which several compounds are potent inhibitors of mutant IDH1 with Ki as low as 420 nM. X-ray crystal structures of IDH1(R132H) in complex with two inhibitors are reported, showing their inhibitor-protein interactions. These compounds can decrease the cellular concentration of D2HG, reduce the levels of histone methylation, and suppress the proliferation of stem-like cancer cells in BT142 glioma with IDH1 R132H mutation.

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Organizational Affiliation: 

Dan L. Duncan Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA.

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
Find proteins for O75874 (Homo sapiens) Explore O75874  Go to UniProtKB:  O75874
NIH Common Fund Data Resources
PHAROS:  O75874 GTEx:  ENSG00000138413

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	A, B	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
42W	A, B	(E)-1-benzyl-5-((1-methyl-5-oxo-2-thioxoimidazolidin-4-ylidene)methyl)pyridin-2(1H)-one C17 H15 N3 O2 S ORESZEYKAHLKRD-NTEUORMPSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
42W	Ki:  12500   nM  BindingDB
42W	Ki:  4600   nM  BindingDB
42W	Ki:  32900   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.29 Å
• R-Value Free: 0.283 
• R-Value Work: 0.226 
• R-Value Observed: 0.229 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.586	α = 90
b = 82.586	β = 90
c = 306.599	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
HKL-2000	data scaling
HKL-2000	data reduction
PHASES	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-01-21 
• Released Date: 2016-07-27 
Deposition Author(s): Zheng, B., Wu, F., Jiang, H., Kogiso, M., Yao, Y., Zhou, C., Li, X., Song, Y.

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Funding Organization	Location	Grant Number
Cancer Prevention and Research Institute of Texas (CPRIT)	United States	RP140469
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R01NS080963

Revision History 

• Version 1.0: 2016-07-27
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.2: 2019-04-24
  Changes: Author supporting evidence, Data collection
• Version 1.3: 2019-12-18
  Changes: Author supporting evidence