6BKY

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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: 10.1021/acs.jmedchem.8b00305
  • Primary Citation of Related Structures:  
    6BKX, 6BKZ, 6BKY, 6BL1, 6BL0, 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 c ...

    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.


    Organizational Affiliation

    ICGM, U332 INSERM, Paris, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Isocitrate dehydrogenase [NADP] cytoplasmic ABCDEF425Homo sapiensMutation(s): 0 
Gene Names: IDH1PICD
EC: 1.1.1.42
Find proteins for O75874 (Homo sapiens)
Explore O75874 
Go to UniProtKB:  O75874
NIH Common Fund Data Resources
PHAROS:  O75874
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
BUSTERrefinement
AutoPROCdata reduction
AutoPROCdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2017-11-09 
  • Released Date: 2018-07-25 
  • Deposition Author(s): Jakob, C.G., Qiu, W.

Revision History 

  • Version 1.0: 2018-07-25
    Type: Initial release
  • Version 1.1: 2018-08-22
    Changes: Data collection, Database references