- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.80 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x R1R: [2-[2-[[1-[4-[(1S)-1-[[5-fluoranyl-4-[(4S)-2-oxidanylidene-4-propan-2-yl-1,3-oxazolidin-3-yl]pyrimidin-2-yl]amino]ethyl]phenyl]piperidin-4-yl]sulfamoyl]ethylsulfanylmethyl]-3-oxidanylidene-propyl]-trimethyl-azanium(Covalent)
- 2 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)
NDP.2: 19 residues within 4Å:- Chain A: K.72, A.74, T.75, I.76, T.77, R.82, N.96, L.288, G.289, E.306, H.309, G.310, T.311, V.312, T.313, R.314, H.315, T.327, N.328
15 PLIP interactions:15 interactions with chain A- Hydrogen bonds: A:K.72, A:T.75, A:T.77, A:T.77, A:R.82, A:R.82, A:N.96, A:E.306, A:G.310, A:T.311, A:V.312, A:N.328, A:N.328
- Salt bridges: A:R.314, A:H.315
NDP.6: 19 residues within 4Å:- Chain B: K.72, A.74, T.75, I.76, T.77, R.82, N.96, L.288, G.289, E.306, H.309, G.310, T.311, V.312, T.313, R.314, H.315, T.327, N.328
19 PLIP interactions:19 interactions with chain B- Hydrogen bonds: B:K.72, B:T.75, B:T.77, B:T.77, B:T.77, B:R.82, B:R.82, B:N.96, B:E.306, B:G.310, B:G.310, B:T.311, B:V.312, B:N.328, B:N.328
- Water bridges: B:Q.283, B:A.331
- Salt bridges: B:R.314, B:H.315
- 5 x GOL: GLYCEROL(Non-functional Binders)
GOL.3: 2 residues within 4Å:- Chain A: K.4, E.351
No protein-ligand interaction detected (PLIP)GOL.7: 7 residues within 4Å:- Chain B: K.65, I.102, L.103, C.297, P.298, D.299, T.302
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:I.102, B:D.299, B:T.302
GOL.8: 5 residues within 4Å:- Chain B: K.345, N.348, N.349, K.350, A.353
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:N.348
GOL.11: 3 residues within 4Å:- Chain B: D.191, H.194, P.298
No protein-ligand interaction detected (PLIP)GOL.12: 2 residues within 4Å:- Chain B: Q.320, K.321
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:Q.320
- Water bridges: B:Q.320
- 5 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
PEG.4: 2 residues within 4Å:- Ligands: R1R.1, R1R.5
No protein-ligand interaction detected (PLIP)PEG.9: 7 residues within 4Å:- Chain B: M.199, S.202, V.296, G.300, R.338, H.342, K.345
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:S.202, B:G.300, B:H.342
PEG.10: 5 residues within 4Å:- Chain B: S.6, G.7, G.8, E.36, D.38
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:G.8
PEG.13: 5 residues within 4Å:- Chain B: E.190, R.222, E.229, I.230, K.233
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:E.190, B:R.222, B:R.222
PEG.14: 3 residues within 4Å:- Chain B: L.201, S.202, K.345
No protein-ligand interaction detected (PLIP)- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Liang, Q. et al., Structure-based discovery of IHMT-IDH1-053 as a potent irreversible IDH1 mutant selective inhibitor. Eur.J.Med.Chem. (2023)
- Release Date
- 2023-05-24
- Peptides
- Isocitrate dehydrogenase [NADP] cytoplasmic: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
DDDB
AAA
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.80 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x R1R: [2-[2-[[1-[4-[(1S)-1-[[5-fluoranyl-4-[(4S)-2-oxidanylidene-4-propan-2-yl-1,3-oxazolidin-3-yl]pyrimidin-2-yl]amino]ethyl]phenyl]piperidin-4-yl]sulfamoyl]ethylsulfanylmethyl]-3-oxidanylidene-propyl]-trimethyl-azanium(Covalent)
- 2 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)
- 5 x GOL: GLYCEROL(Non-functional Binders)
- 5 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Liang, Q. et al., Structure-based discovery of IHMT-IDH1-053 as a potent irreversible IDH1 mutant selective inhibitor. Eur.J.Med.Chem. (2023)
- Release Date
- 2023-05-24
- Peptides
- Isocitrate dehydrogenase [NADP] cytoplasmic: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
DDDB
AAA