SMTL ID : 8c14.1

Aurora A kinase in complex with TPX2-inhibitor 9

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

monomer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: N.142, D.155 Ligands: MG.2, ADP.17 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.155, H2O.4, H2O.4 MG.2: 4 residues within 4Å: Chain A: D.155 Ligands: MG.1, ADP.17, T5L.18 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.155, A:D.155, H2O.1, H2O.1 MG.3: 1 residues within 4Å: Chain A: E.211 No protein-ligand interaction detected (PLIP)

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

SO4.4: 3 residues within 4Å: Chain A: S.223, R.224, H.247 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.223 Salt bridges: A:H.247

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 2 residues within 4Å: Chain A: R.101, K.105 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: R.61, V.160, H.161 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: K.220, E.226 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain A: R.238 Ligand excluded by PLIP CL.9: 1 residues within 4Å: Chain A: G.54 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain A: R.224 Ligand excluded by PLIP

4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.11: 2 residues within 4Å: Chain A: Y.100, E.141 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:E.141 pi-Cation interactions: A:Y.100 DMS.12: 2 residues within 4Å: Chain A: Y.215, Q.216 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.216 DMS.13: 4 residues within 4Å: Chain A: L.11, V.44, R.86, Y.88 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.86 Water bridges: A:Y.29 DMS.14: 4 residues within 4Å: Chain A: G.236, P.262, W.263 Ligands: GOL.21 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.236, A:N.267

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.15: 4 residues within 4Å: Chain A: S.126, M.254, L.255, R.256 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:M.254, A:R.256 Hydrogen bonds: A:R.256 Water bridges: A:H.129, A:L.255 Salt bridges: A:R.256 ACT.16: 4 residues within 4Å: Chain A: R.132, D.188, E.189, K.190 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.189 Hydrogen bonds: A:E.189 Water bridges: A:E.189 Salt bridges: A:R.132

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.17: 19 residues within 4Å: Chain A: L.20, G.21, K.22, G.23, K.24, V.28, A.41, K.43, L.75, E.92, A.94, T.98, E.141, N.142, L.144, D.155 Ligands: MG.1, MG.2, T5L.18 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:K.24, A:E.92, A:A.94, A:D.155 Water bridges: A:K.22, A:K.22, A:F.25, A:T.98, A:T.98, A:E.141, A:E.141, A:N.142, A:D.155, A:D.155, A:D.155 Salt bridges: A:K.43, A:K.43

1 x T5L: (1~{R},2~{R})-cyclohexane-1,2-dicarboxylic acid

T5L.18: 12 residues within 4Å: Chain A: F.25, K.43, L.45, V.55, Q.58, L.59, E.62, D.155, G.157, W.158 Ligands: MG.2, ADP.17 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.25, A:V.55, A:Q.58 Hydrogen bonds: A:E.62 Water bridges: A:F.25, A:G.157, A:W.158 Salt bridges: A:K.43, A:K.43

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.19: 3 residues within 4Å: Chain A: L.106, S.107, K.108 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.106 Water bridges: A:D.110 GOL.20: 4 residues within 4Å: Chain A: D.83, A.84, T.85, R.86 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.83, A:A.84, A:T.85, A:T.85, A:R.86 Water bridges: A:D.83 GOL.21: 5 residues within 4Å: Chain A: D.239, R.243, H.261, P.262 Ligands: DMS.14 No protein-ligand interaction detected (PLIP) GOL.22: 5 residues within 4Å: Chain A: K.47, A.48, E.51, A.84 Ligands: T0L.24 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.48, A:A.84 GOL.23: 5 residues within 4Å: Chain A: R.60, V.63, E.64, Y.80 Ligands: T0L.24 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.64, A:Y.80 Water bridges: A:R.60, A:R.60

1 x T0L: 4-(4-chloranyl-3-cyano-phenyl)-1~{H}-indole-6-carboxylic acid

T0L.24: 11 residues within 4Å: Chain A: K.47, L.50, E.51, L.59, V.63, Y.80, F.81, H.82, V.87 Ligands: GOL.22, GOL.23 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:K.47, A:L.50, A:L.59, A:H.82, A:V.87, A:V.87 Hydrogen bonds: A:E.51, A:E.51 Water bridges: A:K.47 Salt bridges: A:K.47, A:H.82 pi-Stacking: A:H.82 pi-Cation interactions: A:K.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stockwell, S.R. et al., Selective Aurora A-TPX2 Interaction Inhibitors Have In Vivo Efficacy as Targeted Antimitotic Agents. J.Med.Chem. (2024)

Release Date

2024-01-10

Peptides

Aurora kinase A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Aurora kinase A

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