SMTL ID : 4jt3.3 (2 other biounits)

Crystal Structure of TTK kinase domain with an inhibitor: 400740

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

16 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 5 residues within 4Å: Chain A: H.122, H.125, P.199, I.268, P.269 Ligand excluded by PLIP PO4.2: 7 residues within 4Å: Chain A: L.99, K.102, K.103, S.104, I.105, Y.212, G.216 Ligand excluded by PLIP PO4.3: 4 residues within 4Å: Chain A: Y.40, Y.83, Y.85 Ligands: PO4.4 Ligand excluded by PLIP PO4.4: 5 residues within 4Å: Chain A: I.4, F.26, Y.40, Y.85 Ligands: PO4.3 Ligand excluded by PLIP PO4.16: 5 residues within 4Å: Chain B: H.122, H.125, P.199, I.268, P.269 Ligand excluded by PLIP PO4.17: 7 residues within 4Å: Chain B: L.99, K.102, K.103, S.104, I.105, Y.212, G.216 Ligand excluded by PLIP PO4.18: 4 residues within 4Å: Chain B: Y.40, Y.83, Y.85 Ligands: PO4.19 Ligand excluded by PLIP PO4.19: 5 residues within 4Å: Chain B: I.4, F.26, Y.40, Y.85 Ligands: PO4.18 Ligand excluded by PLIP PO4.31: 5 residues within 4Å: Chain C: H.122, H.125, P.199, I.268, P.269 Ligand excluded by PLIP PO4.32: 7 residues within 4Å: Chain C: L.99, K.102, K.103, S.104, I.105, Y.212, G.216 Ligand excluded by PLIP PO4.33: 4 residues within 4Å: Chain C: Y.40, Y.83, Y.85 Ligands: PO4.34 Ligand excluded by PLIP PO4.34: 5 residues within 4Å: Chain C: I.4, F.26, Y.40, Y.85 Ligands: PO4.33 Ligand excluded by PLIP PO4.46: 5 residues within 4Å: Chain D: H.122, H.125, P.199, I.268, P.269 Ligand excluded by PLIP PO4.47: 7 residues within 4Å: Chain D: L.99, K.102, K.103, S.104, I.105, Y.212, G.216 Ligand excluded by PLIP PO4.48: 4 residues within 4Å: Chain D: Y.40, Y.83, Y.85 Ligands: PO4.49 Ligand excluded by PLIP PO4.49: 5 residues within 4Å: Chain D: I.4, F.26, Y.40, Y.85 Ligands: PO4.48 Ligand excluded by PLIP

4 x 1PH: 2-phenyl-N-[3-(3-sulfamoylphenyl)-2H-indazol-5-yl]acetamide(Non-covalent)

1PH.5: 20 residues within 4Å: Chain A: I.17, G.18, S.19, G.20, S.23, V.25, Q.27, A.37, K.39, I.72, M.88, E.89, C.90, G.91, N.92, L.140, I.149 Chain C: L.14, K.15 Ligands: EDO.8 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.17, A:I.17, A:V.25, A:K.39, A:L.140, A:L.140, A:I.149 Hydrogen bonds: A:Q.27, A:K.39, A:G.91, A:N.92 1PH.20: 20 residues within 4Å: Chain B: I.17, G.18, S.19, G.20, S.23, V.25, Q.27, A.37, K.39, I.72, M.88, E.89, C.90, G.91, N.92, L.140, I.149 Chain D: L.14, K.15 Ligands: EDO.23 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:I.17, B:I.17, B:V.25, B:K.39, B:L.140, B:L.140, B:I.149 Hydrogen bonds: B:Q.27, B:K.39, B:G.91, B:N.92 1PH.35: 20 residues within 4Å: Chain A: L.14, K.15 Chain C: I.17, G.18, S.19, G.20, S.23, V.25, Q.27, A.37, K.39, I.72, M.88, E.89, C.90, G.91, N.92, L.140, I.149 Ligands: EDO.38 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:I.17, C:I.17, C:V.25, C:K.39, C:L.140, C:L.140, C:I.149 Hydrogen bonds: C:Q.27, C:K.39, C:G.91, C:N.92 1PH.50: 20 residues within 4Å: Chain B: L.14, K.15 Chain D: I.17, G.18, S.19, G.20, S.23, V.25, Q.27, A.37, K.39, I.72, M.88, E.89, C.90, G.91, N.92, L.140, I.149 Ligands: EDO.53 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:I.17, D:I.17, D:V.25, D:K.39, D:L.140, D:L.140, D:I.149 Hydrogen bonds: D:Q.27, D:K.39, D:G.91, D:N.92

40 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 4 residues within 4Å: Chain A: R.9, Y.11, Y.36, Y.75 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain A: E.119, H.122, L.272 Ligand excluded by PLIP EDO.8: 8 residues within 4Å: Chain A: K.39, E.57, L.61, M.86, M.88, I.149 Ligands: 1PH.5, EDO.10 Ligand excluded by PLIP EDO.9: 1 residues within 4Å: Chain A: Y.77 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: K.39, Y.54, A.154, Q.156 Ligands: EDO.8 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: K.115, E.119 Ligands: EDO.15 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain A: C.90, N.92, V.142, D.143 Chain C: S.12, L.14, L.29 Ligand excluded by PLIP EDO.13: 1 residues within 4Å: Chain A: D.76 Ligand excluded by PLIP EDO.14: 3 residues within 4Å: Chain A: K.24, Y.40, N.42 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: K.115, V.277, Q.278 Ligands: EDO.11 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain B: R.9, Y.11, Y.36, Y.75 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain B: E.119, H.122, L.272 Ligand excluded by PLIP EDO.23: 8 residues within 4Å: Chain B: K.39, E.57, L.61, M.86, M.88, I.149 Ligands: 1PH.20, EDO.25 Ligand excluded by PLIP EDO.24: 1 residues within 4Å: Chain B: Y.77 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain B: K.39, Y.54, A.154, Q.156 Ligands: EDO.23 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain B: K.115, E.119 Ligands: EDO.30 Ligand excluded by PLIP EDO.27: 7 residues within 4Å: Chain B: C.90, N.92, V.142, D.143 Chain D: S.12, L.14, L.29 Ligand excluded by PLIP EDO.28: 1 residues within 4Å: Chain B: D.76 Ligand excluded by PLIP EDO.29: 3 residues within 4Å: Chain B: K.24, Y.40, N.42 Ligand excluded by PLIP EDO.30: 4 residues within 4Å: Chain B: K.115, V.277, Q.278 Ligands: EDO.26 Ligand excluded by PLIP EDO.36: 4 residues within 4Å: Chain C: R.9, Y.11, Y.36, Y.75 Ligand excluded by PLIP EDO.37: 3 residues within 4Å: Chain C: E.119, H.122, L.272 Ligand excluded by PLIP EDO.38: 8 residues within 4Å: Chain C: K.39, E.57, L.61, M.86, M.88, I.149 Ligands: 1PH.35, EDO.40 Ligand excluded by PLIP EDO.39: 1 residues within 4Å: Chain C: Y.77 Ligand excluded by PLIP EDO.40: 5 residues within 4Å: Chain C: K.39, Y.54, A.154, Q.156 Ligands: EDO.38 Ligand excluded by PLIP EDO.41: 3 residues within 4Å: Chain C: K.115, E.119 Ligands: EDO.45 Ligand excluded by PLIP EDO.42: 7 residues within 4Å: Chain A: S.12, L.14, L.29 Chain C: C.90, N.92, V.142, D.143 Ligand excluded by PLIP EDO.43: 1 residues within 4Å: Chain C: D.76 Ligand excluded by PLIP EDO.44: 3 residues within 4Å: Chain C: K.24, Y.40, N.42 Ligand excluded by PLIP EDO.45: 4 residues within 4Å: Chain C: K.115, V.277, Q.278 Ligands: EDO.41 Ligand excluded by PLIP EDO.51: 4 residues within 4Å: Chain D: R.9, Y.11, Y.36, Y.75 Ligand excluded by PLIP EDO.52: 3 residues within 4Å: Chain D: E.119, H.122, L.272 Ligand excluded by PLIP EDO.53: 8 residues within 4Å: Chain D: K.39, E.57, L.61, M.86, M.88, I.149 Ligands: 1PH.50, EDO.55 Ligand excluded by PLIP EDO.54: 1 residues within 4Å: Chain D: Y.77 Ligand excluded by PLIP EDO.55: 5 residues within 4Å: Chain D: K.39, Y.54, A.154, Q.156 Ligands: EDO.53 Ligand excluded by PLIP EDO.56: 3 residues within 4Å: Chain D: K.115, E.119 Ligands: EDO.60 Ligand excluded by PLIP EDO.57: 7 residues within 4Å: Chain B: S.12, L.14, L.29 Chain D: C.90, N.92, V.142, D.143 Ligand excluded by PLIP EDO.58: 1 residues within 4Å: Chain D: D.76 Ligand excluded by PLIP EDO.59: 3 residues within 4Å: Chain D: K.24, Y.40, N.42 Ligand excluded by PLIP EDO.60: 4 residues within 4Å: Chain D: K.115, V.277, Q.278 Ligands: EDO.56 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qiu, W. et al., Crystal Structure of TTK kinase domain with an inhibitor: 400740. 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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