8T7D

Crystal structure of wild type IDH1 bound to compound 1

• PDB DOI: https://doi.org/10.2210/pdb8T7D/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• 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: 3.44 Å
• R-Value Free: 0.267 
• R-Value Work: 0.240 
• R-Value Observed: 0.242 

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 193.87 kDa 
• Atom Count: 11,650 
• Modelled Residue Count: 1,562 
• Deposited Residue Count: 1,696 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isocitrate dehydrogenase [NADP] cytoplasmic	A, B, C, D	424	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 GTEx:  ENSG00000138413

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZT3 (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	N-(4-tert-butylphenyl)-7,8-dimethyl-5,11-dihydro-6H-pyrido[2,3-b][1,5]benzodiazepine-6-carboxamide C25 H28 N4 O RHGZKBFOWYGLDJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.44 Å
• R-Value Free: 0.267 
• R-Value Work: 0.240 
• R-Value Observed: 0.242 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.592	α = 90
b = 120.991	β = 119.39
c = 139.274	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
HKL-2000	data reduction
HKL-2000	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