8T7O

Crystal structure of the R132H mutant of IDH1 bound to AG-120

• PDB DOI: https://doi.org/10.2210/pdb8T7O/pdb

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


• Deposited: 2023-06-20 Released: 2024-08-28 
• 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: 2.05 Å
• R-Value Free: 0.255 
• R-Value Work: 0.224 
• R-Value Observed: 0.225 

Starting Model: experimental

Literature

Mechanistic and Biostructural Studies of Mutant IDH1

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

To be published.

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: 98.17 kDa 
• Atom Count: 6,636 
• Modelled Residue Count: 799 
• 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 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
IV3 (Subject of Investigation/LOI)	D [auth A]	ivosidenib C28 H22 Cl F3 N6 O3 WIJZXSAJMHAVGX-DHLKQENFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.255 
• R-Value Work: 0.224 
• R-Value Observed: 0.225 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.445	α = 90
b = 79.445	β = 90
c = 305.312	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-28 
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: 2024-08-28
  Type: Initial release