SMTL ID : 4ja8.1

Complex of Mitochondrial Isocitrate Dehydrogenase R140Q Mutant with AGI-6780 Inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

2 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.1: 19 residues within 4Å: Chain A: K.72, A.74, T.75, I.76, T.77, R.82, N.96, L.287, H.308, G.309, T.310, V.311, T.312, R.313, H.314, T.326, N.327, D.374 Ligands: GOL.5 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:K.72, A:T.75, A:T.77, A:T.77, A:T.77, A:R.82, A:R.82, A:N.96, A:H.308, 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 NDP.8: 21 residues within 4Å: Chain B: K.72, A.74, T.75, I.76, T.77, R.82, N.96, L.287, G.288, E.305, A.307, H.308, G.309, T.310, V.311, T.312, R.313, H.314, T.326, N.327, D.374 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:K.72, B:T.75, B:T.77, B:T.77, B:R.82, B:R.82, B:N.96, B:E.305, B:G.309, B:T.310, B:V.311, B:N.327, B:N.327 Water bridges: B:T.75, B:T.312, B:T.312, B:T.312 Salt bridges: B:R.313, B:H.314

1 x 1K9: 1-[5-(cyclopropylsulfamoyl)-2-thiophen-3-yl-phenyl]-3-[3-(trifluoromethyl)phenyl]urea(Non-covalent)

1K9.2: 20 residues within 4Å: Chain A: W.124, V.254, V.257, Y.271, D.272, V.275, Q.276, I.279 Chain B: L.120, W.124, V.254, V.257, L.258, W.266, Y.271, D.272, V.275, Q.276, I.279, L.280 16 PLIP interactions: 9 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:L.120, B:W.124, B:L.258, B:V.275, B:I.279, B:L.280, A:V.275, A:I.279, A:I.279 Hydrogen bonds: B:Q.276, B:Q.276, A:Q.276, A:Q.276, A:Q.276 Halogen bonds: B:Q.276, A:Y.271

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 3 residues within 4Å: Chain A: D.274, D.278 Chain B: D.251 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:D.251, A:D.274, H2O.11, H2O.19, H2O.19 CA.9: 3 residues within 4Å: Chain A: D.251 Chain B: D.274, D.278 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.251, B:D.274, B:D.278, H2O.19, H2O.27

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: D.231, K.232, H.233, Y.234, K.235, T.236 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.233, A:K.235, A:T.236, A:T.236 Water bridges: A:D.237 GOL.5: 4 residues within 4Å: Chain A: T.77, S.94, N.96 Ligands: NDP.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.94, A:S.94, A:N.96 GOL.6: 7 residues within 4Å: Chain A: F.144, V.145, A.146, D.147, R.148 Chain B: F.156, K.165 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:V.145, A:D.147, B:K.165 Water bridges: A:R.148 GOL.7: 4 residues within 4Å: Chain A: E.364, T.365, S.368, N.404 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.364 Water bridges: A:K.360

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, F. et al., Targeted inhibition of mutant IDH2 in leukemia cells induces cellular differentiation. Science (2013)

Release Date

2013-04-10

Peptides

Isocitrate dehydrogenase [NADP], mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Isocitrate dehydrogenase [NADP], mitochondrial