6BKX

Novel Modes of Inhibition of Wild-Type IDH1: Direct Covalent Modification of His315 with Cmpd1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 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: 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isocitrate dehydrogenase [NADP] cytoplasmicA [auth C],
B,
C [auth A]
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
GTEx:  ENSG00000138413 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75874
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DWP (Subject of Investigation/LOI)
Query on DWP

Download Ideal Coordinates CCD File 
F [auth C],
H [auth B],
L [auth A]
(6aS,7S,9R,10aS)-7,10a-dimethyl-8-oxo-2-(phenylamino)-5,6,6a,7,8,9,10,10a-octahydrobenzo[h]quinazoline-9-carbonitrile
C21 H22 N4 O
DXKZYIZYBKRROL-IRYHUZONSA-N
ICT
Query on ICT

Download Ideal Coordinates CCD File 
E [auth C],
G [auth B],
K [auth B]
ISOCITRIC ACID
C6 H8 O7
ODBLHEXUDAPZAU-ZAFYKAAXSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth C],
I [auth B],
J [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.301α = 90
b = 274.911β = 90
c = 116.897γ = 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

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