6BKZ

Novel Modes of Inhibition of Wild-Type IDH1: Non-equivalent Allosteric Inhibition with Cmpd3

• PDB DOI:  https://doi.org/10.2210/pdb6BKZ/pdb

• Classification: oxidoreductase/oxidoreductase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.204 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 

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

• PubMed: 30004704 
• 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.

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Organizational Affiliation: 

ICGM, U332 INSERM, Paris, France.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 98.8 kDa 
• Atom Count: 7,439 
• Modelled Residue Count: 824 
• Deposited Residue Count: 850 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isocitrate dehydrogenase [NADP] cytoplasmic	A, B	425	Homo sapiens	Mutation(s): 0  Gene Names: IDH1, PICD 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	C [auth A], E [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
DWM (Subject of Investigation/LOI)	D [auth A], F [auth B]	(7R)-1-[(4-fluorophenyl)methyl]-N-{3-[(1R)-1-hydroxyethyl]phenyl}-7-methyl-5-(1H-pyrrole-2-carbonyl)-4,5,6,7-tetrahydro-1H-pyrazolo[4,3-c]pyridine-3-carboxamide C28 H28 F N5 O3 IVFDDVKCCBDPQZ-QZTJIDSGSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
DWM	Binding MOAD:  6BKZ	IC50: 120 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.204 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.463	α = 90
b = 83.463	β = 90
c = 299.255	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• 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
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description