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 

wwPDB Validation 3D Report Full Report


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

  • 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 demonstr ...

    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

    Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Isocitrate dehydrogenase [NADP] cytoplasmic
A, B
413Homo sapiensMutation(s): 1 
Gene Names: IDH1 (PICD)
EC: 1.1.1.42
Find proteins for O75874 (Homo sapiens)
Go to Gene View: IDH1
Go to UniProtKB:  O75874
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download SDF File 
Download CCD File 
A, B
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
59D
Query on 59D

Download SDF File 
Download CCD File 
A, 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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
59DIC50: 2.9 - 46 nM (99) BINDINGDB
59DIC50: 46 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.220 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 82.726α = 90.00
b = 82.726β = 90.00
c = 303.639γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
HKL-2000data reduction
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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