5DE1

Crystal structure of human IDH1 in complex with GSK321A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

New IDH1 mutant inhibitors for treatment of acute myeloid leukemia.

Okoye-Okafor, U.C.Bartholdy, B.Cartier, J.Gao, E.N.Pietrak, B.Rendina, A.R.Rominger, C.Quinn, C.Smallwood, A.Wiggall, K.J.Reif, A.J.Schmidt, S.J.Qi, H.Zhao, H.Joberty, G.Faelth-Savitski, M.Bantscheff, M.Drewes, G.Duraiswami, C.Brady, P.Groy, A.Narayanagari, S.R.Antony-Debre, I.Mitchell, K.Wang, H.R.Kao, Y.R.Christopeit, M.Carvajal, L.Barreyro, L.Paietta, E.Makishima, H.Will, B.Concha, N.Adams, N.D.Schwartz, B.McCabe, M.T.Maciejewski, J.Verma, A.Steidl, U.

(2015) Nat Chem Biol 11: 878-886

  • DOI: 10.1038/nchembio.1930
  • Primary Citation of Related Structures:  
    5DE1

  • PubMed Abstract: 
  • Neomorphic mutations in isocitrate dehydrogenase 1 (IDH1) are driver mutations in acute myeloid leukemia (AML) and other cancers. We report the development of new allosteric inhibitors of mutant IDH1. Crystallographic and biochemical results demonstrated that compounds of this chemical series bind to an allosteric site and lock the enzyme in a catalytically inactive conformation, thereby enabling inhibition of different clinically relevant IDH1 mutants ...

    Neomorphic mutations in isocitrate dehydrogenase 1 (IDH1) are driver mutations in acute myeloid leukemia (AML) and other cancers. We report the development of new allosteric inhibitors of mutant IDH1. Crystallographic and biochemical results demonstrated that compounds of this chemical series bind to an allosteric site and lock the enzyme in a catalytically inactive conformation, thereby enabling inhibition of different clinically relevant IDH1 mutants. Treatment of IDH1 mutant primary AML cells uniformly led to a decrease in intracellular 2-HG, abrogation of the myeloid differentiation block and induction of granulocytic differentiation at the level of leukemic blasts and more immature stem-like cells, in vitro and in vivo. Molecularly, treatment with the inhibitors led to a reversal of the DNA cytosine hypermethylation patterns caused by mutant IDH1 in the cells of individuals with AML. Our study provides proof of concept for the molecular and biological activity of novel allosteric inhibitors for targeting different mutant forms of IDH1 in leukemia.


    Organizational Affiliation

    Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, New York, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Isocitrate dehydrogenase [NADP] cytoplasmicA, B413Homo sapiensMutation(s): 1 
Gene Names: IDH1PICD
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 
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
NAP
Query on NAP

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
59D
Query on 59D

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
(7R)-1-(4-fluorobenzyl)-N-{3-[(1S)-1-hydroxyethyl]phenyl}-7-methyl-5-(1H-pyrrol-2-ylcarbonyl)-4,5,6,7-tetrahydro-1H-pyrazolo[4,3-c]pyridine-3-carboxamide
C28 H28 F N5 O3
IVFDDVKCCBDPQZ-MSOLQXFVSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
59D BindingDB:  5DE1 IC50: min: 2.9, max: 970 (nM) from 9 assay(s)
EC50: 85 (nM) from 1 assay(s)
Binding MOAD:  5DE1 IC50: 46 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.726α = 90
b = 82.726β = 90
c = 303.639γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-07
    Type: Initial release
  • Version 1.1: 2015-10-21
    Changes: Database references
  • Version 1.2: 2015-10-28
    Changes: Database references