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SMTL ID : 6o2z.1
Crystal structure of IDH1 R132H mutant in complex with compound 32
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 2.50 Å
Oligo State
homo-dimer
Ligands
2 x
LJV
:
6-{[(6-chloro-2-oxo-1,2-dihydroquinolin-3-yl)methyl]amino}-2-methylpyridine-3-carbonitrile
(Non-covalent)
LJV.1:
17 residues within 4Å:
Chain A:
R.109
,
A.111
,
I.113
,
R.119
,
L.120
,
W.124
,
I.128
,
I.130
,
A.258
,
M.259
,
W.267
,
D.279
,
V.281
,
A.282
,
Y.285
,
M.291
Chain B:
S.280
16
PLIP interactions
:
16 interactions with chain A
Hydrophobic interactions:
A:A.111
,
A:I.113
,
A:I.128
,
A:I.130
,
A:I.130
,
A:V.281
,
A:V.281
,
A:V.281
,
A:Y.285
Hydrogen bonds:
A:R.109
,
A:A.111
,
A:L.120
,
A:I.128
,
A:D.279
Water bridges:
A:I.128
,
A:I.128
LJV.4:
17 residues within 4Å:
Chain A:
S.280
Chain B:
R.109
,
A.111
,
I.113
,
R.119
,
L.120
,
W.124
,
I.128
,
I.130
,
A.258
,
M.259
,
W.267
,
D.279
,
V.281
,
A.282
,
Y.285
,
M.291
16
PLIP interactions
:
16 interactions with chain B
Hydrophobic interactions:
B:A.111
,
B:I.113
,
B:W.124
,
B:I.128
,
B:I.130
,
B:V.281
,
B:V.281
,
B:V.281
,
B:Y.285
Hydrogen bonds:
B:A.111
,
B:L.120
,
B:I.128
,
B:D.279
Water bridges:
B:I.128
,
B:I.128
pi-Stacking:
B:W.267
2 x
NAP
:
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
(Non-covalent)
NAP.2:
19 residues within 4Å:
Chain A:
K.72
,
A.74
,
T.75
,
I.76
,
T.77
,
R.82
,
N.96
,
Q.277
,
G.289
,
E.306
,
H.309
,
G.310
,
T.311
,
V.312
,
T.313
,
R.314
,
H.315
,
T.327
,
N.328
20
PLIP interactions
:
20 interactions with chain A
Hydrogen bonds:
A:K.72
,
A:T.75
,
A:T.75
,
A:T.77
,
A:T.77
,
A:T.77
,
A:R.82
,
A:R.82
,
A:H.309
,
A:G.310
,
A:G.310
,
A:T.311
,
A:V.312
,
A:T.313
,
A:N.328
Water bridges:
A:T.313
,
A:R.314
,
A:A.331
Salt bridges:
A:R.314
,
A:H.315
NAP.5:
21 residues within 4Å:
Chain B:
K.72
,
A.74
,
T.75
,
I.76
,
T.77
,
R.82
,
N.96
,
Q.277
,
S.287
,
G.289
,
E.306
,
H.309
,
G.310
,
T.311
,
V.312
,
T.313
,
R.314
,
H.315
,
T.327
,
N.328
,
D.375
20
PLIP interactions
:
20 interactions with chain B
Hydrogen bonds:
B:K.72
,
B:K.72
,
B:T.75
,
B:T.75
,
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:T.313
,
B:N.328
,
B:N.328
Salt bridges:
B:R.314
,
B:H.315
pi-Stacking:
B:H.309
2 x
GOL
:
GLYCEROL
(Non-functional Binders)
GOL.3:
5 residues within 4Å:
Chain A:
S.6
,
G.7
,
G.8
,
E.36
,
D.38
2
PLIP interactions
:
2 interactions with chain A
Hydrogen bonds:
A:G.7
,
A:G.8
GOL.6:
5 residues within 4Å:
Chain B:
S.6
,
G.7
,
G.8
,
E.36
,
D.38
4
PLIP interactions
:
4 interactions with chain B
Hydrogen bonds:
B:G.7
,
B:G.8
,
B:E.36
,
B:D.38
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Lin, J. et al., Discovery and Optimization of Quinolinone Derivatives as Potent, Selective, and Orally Bioavailable Mutant Isocitrate Dehydrogenase 1 (mIDH1) Inhibitors. J.Med.Chem. (2019)
Release Date
2019-06-26
Peptides
Isocitrate dehydrogenase [NADP] cytoplasmic:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
B
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Isocitrate dehydrogenase [NADP] cytoplasmic
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