Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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: homology

Macromolecule Content

• Total Structure Weight: 94.01 kDa 
• Atom Count: 6475 
• Modelled Residue Count: 811 
• Deposited Residue Count: 828 
• Unique protein chains: 1

6Q6F

Crystal structure of IDH1 R132H in complex with HMS101

• PDB DOI: 10.2210/pdb6Q6F/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-12-10 Released: 2019-10-16 
• Deposition Author(s): Chaturvedi, A., Goparaju, R., Gupta, C., Kluenemann, T., Araujo Cruz, M.M., Kloos, A., Goerlich, K., Schottmann, R., Struys, E.A., Ganser, A., Preller, M., Heuser, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.288 
• R-Value Work: 0.232 
• R-Value Observed: 0.235 

Literature

In vivo efficacy of mutant IDH1 inhibitor HMS-101 and structural resolution of distinct binding site.

Chaturvedi, A., Goparaju, R., Gupta, C., Weder, J., Klunemann, T., Araujo Cruz, M.M., Kloos, A., Goerlich, K., Schottmann, R., Othman, B., Struys, E.A., Bahre, H., Grote-Koska, D., Brand, K., Ganser, A., Preller, M., Heuser, M.

(2020) Leukemia 34: 416-426

• PubMed: 31586149 
• DOI: 10.1038/s41375-019-0582-x
• Primary Citation of Related Structures:  
  6Q6F


• PubMed Abstract: 
  

Mutations in isocitrate dehydrogenase 1 (IDH1) are found in 6% of AML patients. Mutant IDH produces R-2-hydroxyglutarate (R-2HG), which induces histone- and DNA-hypermethylation through the inhibition of epigenetic regulators, thus linking metabolism to tumorigenesis. Here we report the biochemical characterization, in vivo antileukemic effects, structural binding, and molecular mechanism of the inhibitor HMS-101, which inhibits the enzymatic activity of mutant IDH1 (IDH1mut). Treatment of IDH1mut primary AML cells reduced 2-hydroxyglutarate levels (2HG) and induced myeloid differentiation in vitro. Co-crystallization of HMS-101 and mutant IDH1 revealed that HMS-101 binds to the active site of IDH1mut in close proximity to the regulatory segment of the enzyme in contrast to other IDH1 inhibitors. HMS-101 also suppressed 2HG production, induced cellular differentiation and prolonged survival in a syngeneic mutant IDH1 mouse model and a patient-derived human AML xenograft model in vivo. Cells treated with HMS-101 showed a marked upregulation of the differentiation-associated transcription factors CEBPA and PU.1, and a decrease in cell cycle regulator cyclin A2. In addition, the compound attenuated histone hypermethylation. Together, HMS-101 is a unique inhibitor that binds to the active site of IDH1mut directly and is active in IDH1mut preclinical models.

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Organizational Affiliation: 

Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isocitrate dehydrogenase [NADP] cytoplasmic	A, B	414	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HJQ (Subject of Investigation/LOI)	C [auth A], D [auth B]	(2~{R})-2-[2-[(3~{R})-3-(4-fluorophenyl)pyrrolidin-1-yl]ethyl]-1,4-dimethyl-piperazine C18 H28 F N3 CWUVXNOWKCDEGI-FUHWJXTLSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.288 
• R-Value Work: 0.232 
• R-Value Observed: 0.235 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.396	α = 90
b = 82.396	β = 90
c = 301.43	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2018-12-10 
• Released Date: 2019-10-16 
Deposition Author(s): Chaturvedi, A., Goparaju, R., Gupta, C., Kluenemann, T., Araujo Cruz, M.M., Kloos, A., Goerlich, K., Schottmann, R., Struys, E.A., Ganser, A., Preller, M., Heuser, M.

Revision History  

• Version 1.0: 2019-10-16
  Type: Initial release
  
• Version 1.1: 2020-02-12
  Changes: Database references