5L57

Crystal structure of Iso-citrate Dehydrogenase R132H in complex with a novel inhibitor (compound 13a)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

Discovery and Optimization of Allosteric Inhibitors of Mutant Isocitrate Dehydrogenase 1 (R132H IDH1) Displaying Activity in Human Acute Myeloid Leukemia Cells.

Jones, S., Ahmet, J., Ayton, K., Ball, M., Cockerill, M., Fairweather, E., Hamilton, N., Harper, P., Hitchin, J., Jordan, A., Levy, C., Lopez, R., McKenzie, E., Packer, M., Plant, D., Simpson, I., Simpson, P., Sinclair, I., Somervaille, T.C., Small, H., Spencer, G.J., Thomson, G., Tonge, M., Waddell, I., Walsh, J., Waszkowycz, B., Wigglesworth, M., Wiseman, D.H., Ogilvie, D.

(2016) J Med Chem 59: 11120-11137

  • DOI: https://doi.org/10.1021/acs.jmedchem.6b01320
  • Primary Citation of Related Structures:  
    5L57, 5L58

  • PubMed Abstract: 

    • A collaborative high throughput screen of 1.35 million compounds against mutant (R132H) isocitrate dehydrogenase IDH1 led to the identification of a novel series of inhibitors. Elucidation of the bound ligand crystal structure showed that the inhibitors exhibited a novel binding mode in a previously identified allosteric site of IDH1 (R132H) ...

    A collaborative high throughput screen of 1.35 million compounds against mutant (R132H) isocitrate dehydrogenase IDH1 led to the identification of a novel series of inhibitors. Elucidation of the bound ligand crystal structure showed that the inhibitors exhibited a novel binding mode in a previously identified allosteric site of IDH1 (R132H). This information guided the optimization of the series yielding submicromolar enzyme inhibitors with promising cellular activity. Encouragingly, one compound from this series was found to induce myeloid differentiation in primary human IDH1 R132H AML cells in vitro.

    Organizational Affiliation: 

    Manchester Institute of Biotechnology, University of Manchester , Princess Street, Manchester, M1 7DN, U.K.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Isocitrate dehydrogenase [NADP] cytoplasmic414Homo sapiensMutation(s): 6 
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75874
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP
Download Ideal Coordinates CCD File 
B [auth A]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N		 Ligand Interaction
6N3
Query on 6N3
Download Ideal Coordinates CCD File 
C [auth A](1~{R},5~{S})-3-[6-(3-methylbutoxy)-5-[[(1~{R},3~{S})-5-oxidanyl-2-adamantyl]carbamoyl]pyridin-2-yl]-3-azabicyclo[3.1.0]hexane-6-carboxylic acid
C27 H37 N3 O5
IXFGEDLOELTAGL-XVRJTNSXSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.218 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.866α = 90
b = 72.866β = 90
c = 182.642γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

  • Released Date: 2016-12-14 
    • Deposition Author(s): Levy, C.

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-14
    Type: Initial release
  • Version 1.1: 2017-01-11
    Changes: Database references
  • Version 1.2: 2019-10-09
    Changes: Data collection, Database references