SMTL ID : 5de1.1

Crystal structure of human IDH1 in complex with GSK321A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 18 residues within 4Å: Chain A: K.71, T.74, I.75, T.76, R.81, N.95, G.288, E.305, H.308, G.309, T.310, V.311, T.312, R.313, H.314, T.326, N.327, D.374 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:K.71, A:T.74, A:T.74, A:T.76, A:T.76, A:T.76, A:R.81, A:R.81, A:N.95, A:G.309, A:G.309, A:T.310, A:V.311, A:N.327, A:N.327 Water bridges: A:A.330 Salt bridges: A:R.313, A:H.314 NAP.3: 19 residues within 4Å: Chain A: K.259 Chain B: K.71, A.73, T.74, I.75, T.76, R.81, N.95, G.288, E.305, H.308, G.309, T.310, V.311, T.312, R.313, H.314, T.326, N.327 20 PLIP interactions: 19 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.74, B:T.74, B:T.76, B:T.76, B:R.81, B:R.81, B:N.95, B:G.309, B:G.309, B:T.310, B:V.311, B:N.327, B:N.327 Water bridges: B:T.74, B:E.305, B:E.305, B:A.330 Salt bridges: B:R.313, B:H.314, A:K.259

2 x 59D: (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(Non-covalent)

59D.2: 19 residues within 4Å: Chain A: A.110, I.112, P.117, R.118, L.119, W.123, K.125, P.126, I.127, I.129, W.266, V.280, A.281, G.283, Y.284, M.290, C.378 Chain B: L.119 Ligands: 59D.4 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.110, A:I.112, A:L.119, A:W.123, A:I.127, A:I.129, A:W.266, A:V.280, B:L.119 Hydrogen bonds: A:L.119, A:K.125, A:I.127, A:V.280, A:Y.284 pi-Stacking: A:W.123, A:Y.284 59D.4: 18 residues within 4Å: Chain A: L.119 Chain B: A.110, I.112, P.117, R.118, L.119, W.123, K.125, P.126, I.127, I.129, W.266, V.280, A.281, G.283, Y.284, M.290 Ligands: 59D.2 18 PLIP interactions: 17 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.112, B:R.118, B:L.119, B:L.119, B:W.123, B:I.127, B:I.129, B:W.266, B:V.280, B:V.280, A:L.119 Hydrogen bonds: B:L.119, B:K.125, B:I.127, B:V.280, B:Y.284 pi-Stacking: B:W.123, B:Y.284

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Okoye-Okafor, U.C. et al., New IDH1 mutant inhibitors for treatment of acute myeloid leukemia. Nat.Chem.Biol. (2015)

Release Date

2015-10-07

Peptides

Isocitrate dehydrogenase [NADP] cytoplasmic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Isocitrate dehydrogenase [NADP] cytoplasmic