Novel Binding Modes of Inhibition of Wild-Type IDH1: Allosteric Inhibition with Cmpd2

Experimental Data Snapshot

  • Resolution: 2.17 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

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Novel Modes of Inhibition of Wild-Type Isocitrate Dehydrogenase 1 (IDH1): Direct Covalent Modification of His315.

Jakob, C.G.Upadhyay, A.K.Donner, P.L.Nicholl, E.Addo, S.N.Qiu, W.Ling, C.Gopalakrishnan, S.M.Torrent, M.Cepa, S.P.Shanley, J.Shoemaker, A.R.Sun, C.C.Vasudevan, A.Woller, K.R.Shotwell, J.B.Shaw, B.Bian, Z.Hutti, J.E.

(2018) J Med Chem 61: 6647-6657

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b00305
  • Primary Citation of Related Structures:  
    6BKX, 6BKY, 6BKZ, 6BL0, 6BL1, 6BL2

  • PubMed Abstract: 

    IDH1 plays a critical role in a number of metabolic processes and serves as a key source of cytosolic NADPH under conditions of cellular stress. However, few inhibitors of wild-type IDH1 have been reported. Here we present the discovery and biochemical characterization of two novel inhibitors of wild-type IDH1. In addition, we present the first ligand-bound crystallographic characterization of these novel small molecule IDH1 binding pockets. Importantly, the NADPH competitive α,β-unsaturated enone 1 makes a unique covalent linkage through active site H315. As few small molecules have been shown to covalently react with histidine residues, these data support the potential utility of an underutilized strategy for reversible covalent small molecule design.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isocitrate dehydrogenase [NADP] cytoplasmic425Homo sapiensMutation(s): 0 
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
K32 (Subject of Investigation/LOI)
Query on K32

Download Ideal Coordinates CCD File 
I [auth D],
N [auth A],
P [auth E]
C7 H2 Br4 N2 O
Query on LMR

Download Ideal Coordinates CCD File 
G [auth D],
K [auth F],
O [auth A]
(2S)-2-hydroxybutanedioic acid
C4 H6 O5
Query on MG

Download Ideal Coordinates CCD File 
H [auth D],
J [auth D],
L [auth F],
M [auth A]
Binding Affinity Annotations 
IDSourceBinding Affinity
K32 Binding MOAD:  6BKY IC50: 270 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.17 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.665α = 90
b = 274.889β = 90
c = 116.798γ = 90
Software Package:
Software NamePurpose
autoPROCdata reduction
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: 2018-07-25
    Type: Initial release
  • Version 1.1: 2018-08-22
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description