IDH1 R132H mutant in complex with IDH305

Experimental Data Snapshot

  • Resolution: 2.33 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

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Discovery and Evaluation of Clinical Candidate IDH305, a Brain Penetrant Mutant IDH1 Inhibitor.

Cho, Y.S.Levell, J.R.Liu, G.Caferro, T.Sutton, J.Shafer, C.M.Costales, A.Manning, J.R.Zhao, Q.Sendzik, M.Shultz, M.Chenail, G.Dooley, J.Villalba, B.Farsidjani, A.Chen, J.Kulathila, R.Xie, X.Dodd, S.Gould, T.Liang, G.Heimbach, T.Slocum, K.Firestone, B.Pu, M.Pagliarini, R.Growney, J.D.

(2017) ACS Med Chem Lett 8: 1116-1121

  • DOI: https://doi.org/10.1021/acsmedchemlett.7b00342
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Inhibition of mutant IDH1 is being evaluated clinically as a promising treatment option for various cancers with hotspot mutation at Arg 132 . Having identified an allosteric, induced pocket of IDH1 R132H , we have explored 3-pyrimidin-4-yl-oxazolidin-2-ones as mutant IDH1 inhibitors for in vivo modulation of 2-HG production and potential brain penetration. We report here optimization efforts toward the identification of clinical candidate IDH305 ( 13 ), a potent and selective mutant IDH1 inhibitor that has demonstrated brain exposure in rodents. Preclinical characterization of this compound exhibited in vivo correlation of 2-HG reduction and efficacy in a patient-derived IDH1 mutant xenograft tumor model. IDH305 ( 13 ) has progressed into human clinical trials for the treatment of cancers with IDH1 mutation.

  • Organizational Affiliation

    Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isocitrate dehydrogenase [NADP] cytoplasmicA,
B [auth C],
C [auth B],
417Homo sapiensMutation(s): 1 
Gene Names: IDH1PICD
UniProt & NIH Common Fund Data Resources
Find proteins for O75874 (Homo sapiens)
Explore O75874 
Go to UniProtKB:  O75874
PHAROS:  O75874
GTEx:  ENSG00000138413 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75874
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NDP

Download Ideal Coordinates CCD File 
E [auth A],
I [auth C],
L [auth B],
O [auth D]
C21 H30 N7 O17 P3
Query on C81

Download Ideal Coordinates CCD File 
F [auth A]
H [auth A]
J [auth C]
M [auth B]
P [auth D]
F [auth A],
H [auth A],
J [auth C],
M [auth B],
P [auth D],
R [auth D]
C23 H22 F4 N6 O2
Query on FLC

Download Ideal Coordinates CCD File 
G [auth A],
K [auth C],
N [auth B],
Q [auth D]
C6 H5 O7
Binding Affinity Annotations 
IDSourceBinding Affinity
C81 Binding MOAD:  6B0Z IC50: 18 (nM) from 1 assay(s)
BindingDB:  6B0Z IC50: min: 11, max: 1.72e+4 (nM) from 14 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.33 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.495α = 90
b = 155.312β = 90
c = 163.054γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata processing
autoPROCdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-08
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Data collection, Database references, Refinement description