6BL2

Novel Modes of Inhibition of Wild-Type IDH1: Direct Covalent Modification of His315 with Cmpd15


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.180 

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:  

  • 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 biochemic ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Isocitrate dehydrogenase [NADP] cytoplasmic
A, B, C
425Homo sapiensMutation(s): 0 
Gene Names: IDH1 (PICD)
EC: 1.1.1.42
Find proteins for O75874 (Homo sapiens)
Go to Gene View: IDH1
Go to UniProtKB:  O75874
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DWS
Query on DWS

Download SDF File 
Download CCD File 
A, B, C
3-[(6aS,7S,9S,10aS)-9-cyano-7-methyl-8-oxo-2-(phenylamino)-6,6a,7,8,9,10-hexahydrobenzo[h]quinazolin-10a(5H)-yl]benzoic acid
C27 H24 N4 O3
MJZJSVVSZUVNQP-RIMKCHMMSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
ICT
Query on ICT

Download SDF File 
Download CCD File 
A, B
ISOCITRIC ACID
C6 H8 O7
ODBLHEXUDAPZAU-ZAFYKAAXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.180 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 95.508α = 90.00
b = 274.889β = 90.00
c = 116.143γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
AutoPROCdata reduction
AutoPROCdata scaling
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Data collection, Database references