SMTL ID : 4js8.3 (2 other biounits)

Crystal structure of TTK kinase domain with an inhibitor: 401348

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-tetramer

Ligands

4 x 1PF: 4-(CYCLOHEXYLMETHOXY)-3-{4-[(1-METHYLPIPERIDIN-4-YL)OXY]PHENYL}-2H-INDAZOLE

1PF.1: 18 residues within 4Å: Chain A: I.17, V.25, A.37, I.72, M.88, E.89, C.90, G.91, N.92, I.93, D.94, S.97, A.137, L.140, I.149, P.159, T.161 Ligands: PEG.4 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.17, A:I.17, A:V.25, A:I.72, A:I.93, A:L.140, A:I.149, A:P.159 Hydrogen bonds: A:G.91, A:D.94 Salt bridges: A:D.94 1PF.8: 18 residues within 4Å: Chain B: I.17, V.25, A.37, I.72, M.88, E.89, C.90, G.91, N.92, I.93, D.94, S.97, A.137, L.140, I.149, P.159, T.161 Ligands: PEG.11 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:I.17, B:I.17, B:V.25, B:I.72, B:I.93, B:L.140, B:I.149, B:P.159 Hydrogen bonds: B:G.91, B:D.94 Salt bridges: B:D.94 1PF.15: 18 residues within 4Å: Chain C: I.17, V.25, A.37, I.72, M.88, E.89, C.90, G.91, N.92, I.93, D.94, S.97, A.137, L.140, I.149, P.159, T.161 Ligands: PEG.18 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:I.17, C:I.17, C:V.25, C:I.72, C:I.93, C:L.140, C:I.149, C:P.159 Hydrogen bonds: C:G.91, C:D.94, C:D.94 Salt bridges: C:D.94 1PF.22: 18 residues within 4Å: Chain D: I.17, V.25, A.37, I.72, M.88, E.89, C.90, G.91, N.92, I.93, D.94, S.97, A.137, L.140, I.149, P.159, T.161 Ligands: PEG.25 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:I.17, D:I.17, D:V.25, D:I.72, D:I.93, D:L.140, D:I.149, D:P.159 Hydrogen bonds: D:G.91, D:D.94, D:D.94 Salt bridges: D:D.94

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: I.4, F.26, Y.40, Y.85 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.85, A:Y.85 SO4.3: 3 residues within 4Å: Chain A: C.256, I.266, E.270 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.270 SO4.9: 4 residues within 4Å: Chain B: I.4, F.26, Y.40, Y.85 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.85, B:Y.85 SO4.10: 3 residues within 4Å: Chain B: C.256, I.266, E.270 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.270 SO4.16: 4 residues within 4Å: Chain C: I.4, F.26, Y.40, Y.85 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.85 SO4.17: 3 residues within 4Å: Chain C: C.256, I.266, E.270 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.270 SO4.23: 4 residues within 4Å: Chain D: I.4, F.26, Y.40, Y.85 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.85 SO4.24: 3 residues within 4Å: Chain D: C.256, I.266, E.270 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.270

8 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 8 residues within 4Å: Chain A: K.39, E.57, L.61, M.86, M.88, I.149, D.150 Ligands: 1PF.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.39 PEG.5: 4 residues within 4Å: Chain A: K.115, E.119, H.122, L.272 No protein-ligand interaction detected (PLIP) PEG.11: 8 residues within 4Å: Chain B: K.39, E.57, L.61, M.86, M.88, I.149, D.150 Ligands: 1PF.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.39 PEG.12: 4 residues within 4Å: Chain B: K.115, E.119, H.122, L.272 No protein-ligand interaction detected (PLIP) PEG.18: 8 residues within 4Å: Chain C: K.39, E.57, L.61, M.86, M.88, I.149, D.150 Ligands: 1PF.15 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.39, C:D.150 PEG.19: 4 residues within 4Å: Chain C: K.115, E.119, H.122, L.272 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.122 PEG.25: 8 residues within 4Å: Chain D: K.39, E.57, L.61, M.86, M.88, I.149, D.150 Ligands: 1PF.22 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.39, D:D.150 PEG.26: 4 residues within 4Å: Chain D: K.115, E.119, H.122, L.272 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.122

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: L.258, K.259, R.260, D.261 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.260, A:R.260, A:D.261 GOL.7: 5 residues within 4Å: Chain A: R.9, Y.11, Y.36, Y.75, D.76 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.9, A:Y.11, A:Y.36, A:D.76 GOL.13: 4 residues within 4Å: Chain B: L.258, K.259, R.260, D.261 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.260, B:R.260, B:D.261 GOL.14: 5 residues within 4Å: Chain B: R.9, Y.11, Y.36, Y.75, D.76 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.9, B:Y.11, B:Y.36, B:D.76 GOL.20: 4 residues within 4Å: Chain C: L.258, K.259, R.260, D.261 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.260, C:R.260, C:D.261 GOL.21: 5 residues within 4Å: Chain C: R.9, Y.11, Y.36, Y.75, D.76 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.9, C:Y.11, C:Y.36, C:D.76, C:D.76 GOL.27: 4 residues within 4Å: Chain D: L.258, K.259, R.260, D.261 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.260, D:R.260, D:D.261 GOL.28: 5 residues within 4Å: Chain D: R.9, Y.11, Y.36, Y.75, D.76 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.9, D:Y.11, D:Y.36, D:D.76, D:D.76

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qiu, W. et al., Crystal structure of TTK kinase domain with an inhibitor: 401348. To be Published

Release Date

2014-03-26

Peptides

Dual specificity protein kinase TTK: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Dual specificity protein kinase TTK

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