6BL1

Novel Modes of Inhibition of Wild-Type IDH1: Direct Covalent Modification of His315 with Cmpd13


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

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Ligand Structure Quality Assessment 


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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 characterization of two novel inhibitors of wild-type IDH1 ...

    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] cytoplasmicC [auth A], A [auth B], B [auth C]425Homo sapiensMutation(s): 0 
Gene Names: IDH1PICD
EC: 1.1.1.42
UniProt & NIH Common Fund Data Resources
Find proteins for O75874 (Homo sapiens)
Explore O75874 
Go to UniProtKB:  O75874
PHAROS:  O75874
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DWG (Subject of Investigation/LOI)
Query on DWG

Download Ideal Coordinates CCD File 
E [auth B], K [auth C], L [auth A](6aS,7S,9S,10aS)-7-methyl-8-oxo-10a-phenyl-2-(phenylamino)-5,6,6a,7,8,9,10,10a-octahydrobenzo[h]quinazoline-9-carbonitrile
C26 H24 N4 O
ZJPWPENZDAACRJ-BXZAVOJSSA-N
 Ligand Interaction
ICT (Subject of Investigation/LOI)
Query on ICT

Download Ideal Coordinates CCD File 
D [auth B], H [auth B], J [auth C]ISOCITRIC ACID
C6 H8 O7
ODBLHEXUDAPZAU-ZAFYKAAXSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
F [auth B], G [auth B], I [auth C]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
DWG Binding MOAD:  6BL1 IC50: 110 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.61α = 90
b = 273.806β = 90
c = 114.786γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
AutoPROCdata reduction
AutoPROCdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

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

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