6Q6F

Crystal structure of IDH1 R132H in complex with HMS101

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 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


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

  • 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 ...

    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.

    Organizational Affiliation: 

    Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany. heuser.michael@mh-hannover.de.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Isocitrate dehydrogenase [NADP] cytoplasmic A, B414Homo sapiensMutation(s): 1 
Gene Names: IDH1, PICD
EC: 1.1.1.42
Find proteins for O75874 (Homo sapiens)
Explore O75874 
Go to UniProtKB:  O75874
NIH Common Fund Data Resources
PHAROS:  O75874
GTEx:  ENSG00000138413
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HJQ
Query on HJQ
Download Ideal Coordinates CCD File 
A, 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		 Ligand Interaction
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 = 82.396α = 90
b = 82.396β = 90
c = 301.43γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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