9B81 | pdb_00009b81

Crystal structure of wild type IDH1 bound to compound 4

• PDB DOI: https://doi.org/10.2210/pdb9B81/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-03-28 Released: 2025-03-26 
• Deposition Author(s): Lu, J., Abeywickrema, P., Heo, M.R., Parthasarathy, G., McCoy, M., Soisson, S.M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.56 Å
• R-Value Free: 
  0.233 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Biostructural, biochemical and biophysical studies of mutant IDH1.

McCoy, M.A., Lu, J., Richard Miller, F., Soisson, S.M., Lam, M.H., Fischer, C.

(2024) Nat Commun 15: 7877-7877

• PubMed: 39251618 
• DOI: https://doi.org/10.1038/s41467-024-51692-0
• Primary Citation of Related Structures:  
  8T7D, 8T7N, 8T7O, 9B81


• PubMed Abstract: 
  

  We report bio-structural, bio-chemical and bio-physical evidence demonstrating how small molecules can bind to both wild-type and mutant IDH1, but only inhibit the enzymatic activity of the mutant isoform. Enabled through x-ray crystallography, we characterized a series of small molecule inhibitors that bound to mutant IDH1 differently than the marketed inhibitor Ivosidenib, for which we have determined the x-ray crystal structure. Across the industry several mutant IDH1 inhibitor chemotypes bind to this allosteric IDH1 pocket and selectively inhibit the mutant enzyme. Detailed characterization by a variety of biophysical techniques and NMR studies led us to propose how compounds binding in the allosteric IDH1 R132H pocket inhibit the production of 2-Hydroxy glutarate.

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Organizational Affiliation: 

MRL, Merck & Co., Inc., Rahway, NJ, USA. [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 98.64 kDa 
• Atom Count: 6,244 
• Modeled Residue Count: 781 
• Deposited Residue Count: 848 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isocitrate dehydrogenase [NADP] cytoplasmic	A, B	424	Homo sapiens	Mutation(s): 1  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 GTEx:  ENSG00000138413

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	D [auth A], G [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
A1AI4 (Subject of Investigation/LOI)	C [auth A], F [auth B]	2-methyl-2-(6-{4-[(2S)-1,1,1-trifluoro-2-hydroxypropan-2-yl]benzoyl}-6,11-dihydro-5H-pyrido[2,3-b][1,5]benzodiazepin-8-yl)propanenitrile C26 H23 F3 N4 O2 ARTKCJPBKAKQRY-VWLOTQADSA-N
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.56 Å
• R-Value Free:  0.233 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.79	α = 90
b = 82.79	β = 90
c = 302.16	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-26 
Deposition Author(s): Lu, J., Abeywickrema, P., Heo, M.R., Parthasarathy, G., McCoy, M., Soisson, S.M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-03-26
  Type: Initial release