Crystal structure of IDH1 R132H mutant in complex with compound 24

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 

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Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Discovery and Optimization of Quinolinone Derivatives as Potent, Selective, and Orally Bioavailable Mutant Isocitrate Dehydrogenase 1 (mIDH1) Inhibitors.

Lin, J.Lu, W.Caravella, J.A.Campbell, A.M.Diebold, R.B.Ericsson, A.Fritzen, E.Gustafson, G.R.Lancia Jr., D.R.Shelekhin, T.Wang, Z.Castro, J.Clarke, A.Gotur, D.Josephine, H.R.Katz, M.Diep, H.Kershaw, M.Yao, L.Kauffman, G.Hubbs, S.E.Luke, G.P.Toms, A.V.Wang, L.Bair, K.W.Barr, K.J.Dinsmore, C.Walker, D.Ashwell, S.

(2019) J Med Chem 62: 6575-6596

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b00362
  • Primary Citation of Related Structures:  
    6O2Y, 6O2Z

  • PubMed Abstract: 

    Mutations at the arginine residue (R132) in isocitrate dehydrogenase 1 (IDH1) are frequently identified in various human cancers. Inhibition of mutant IDH1 (mIDH1) with small molecules has been clinically validated as a promising therapeutic treatment for acute myeloid leukemia and multiple solid tumors. Herein, we report the discovery and optimization of a series of quinolinones to provide potent and orally bioavailable mIDH1 inhibitors with selectivity over wild-type IDH1. The X-ray structure of an early lead 24 in complex with mIDH1-R132H shows that the inhibitor unexpectedly binds to an allosteric site. Efforts to improve the in vitro and in vivo absorption, distribution, metabolism, and excretion (ADME) properties of 24 yielded a preclinical candidate 63 . The detailed preclinical ADME and pharmacology studies of 63 support further development of quinolinone-based mIDH1 inhibitors as therapeutic agents in human trials.

  • Organizational Affiliation

    Forma Therapeutics, Inc. , 500 Arsenal Street, Suite 100 , Watertown , Massachusetts 02472 , United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isocitrate dehydrogenase [NADP] cytoplasmic
A, B, C
425Homo sapiensMutation(s): 1 
Gene Names: IDH1PICD
UniProt & NIH Common Fund Data Resources
Find proteins for O75874 (Homo sapiens)
Explore O75874 
Go to UniProtKB:  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 NAP

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
J [auth C]
C21 H28 N7 O17 P3
LJY (Subject of Investigation/LOI)
Query on LJY

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B],
I [auth C]
C18 H14 Cl N3 O2
Query on BME

Download Ideal Coordinates CCD File 
C2 H6 O S
Binding Affinity Annotations 
IDSourceBinding Affinity
LJY BindingDB:  6O2Y IC50: min: 127, max: 1.00e+5 (nM) from 9 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 165.679α = 90
b = 63.496β = 99.52
c = 143.598γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.2: 2019-08-07
    Changes: Data collection, Database references
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references