SMTL ID : 8c1g.1

Aurora A kinase in complex with TPX2-inhibitor 7

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

monomer

Ligands

1 x T3I: 4-(4-chlorophenyl)-~{N}-(dimethylsulfamoyl)-7-methyl-1~{H}-indole-6-carboxamide

T3I.1: 12 residues within 4Å: Chain A: K.43, L.46, E.47, E.52, L.55, R.56, V.59, Y.76, H.78, D.79, V.83 Ligands: SO4.11 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:K.43, A:K.43, A:L.46, A:E.52, A:L.55, A:R.56, A:Y.76, A:V.83, A:V.83 Hydrogen bonds: A:K.43, A:K.43, A:E.47, A:E.47 Water bridges: A:R.56 pi-Stacking: A:H.78 pi-Cation interactions: A:K.43

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

ADP.2: 20 residues within 4Å: Chain A: L.16, G.17, K.18, G.19, K.20, V.24, A.37, K.39, L.71, E.88, Y.89, A.90, T.94, E.137, N.138, L.140, D.151 Ligands: MG.3, MG.4, T5L.6 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:K.20, A:E.88, A:A.90 Water bridges: A:F.21, A:E.137, A:E.137, A:E.137, A:E.137, A:N.138, A:N.138, A:D.151, A:D.151 Salt bridges: A:K.39, A:K.39

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: N.138, D.151 Ligands: ADP.2, MG.4 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.151, H2O.3, H2O.3 MG.4: 5 residues within 4Å: Chain A: D.133, D.151 Ligands: ADP.2, MG.3, T5L.6 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.151, A:D.151, H2O.1, H2O.3

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: V.59, S.63, Y.74, G.75, Y.76 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.63, A:S.63, A:Y.76, A:Y.76

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

T5L.6: 13 residues within 4Å: Chain A: K.20, F.21, K.39, L.41, V.51, Q.54, L.55, E.58, D.151, G.153, W.154 Ligands: ADP.2, MG.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.21, A:F.21, A:V.51, A:V.51, A:Q.54, A:W.154 Hydrogen bonds: A:E.58 Water bridges: A:W.154 Salt bridges: A:K.39, A:K.39

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

SO4.7: 2 residues within 4Å: Chain A: Q.212, K.216 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.213 Salt bridges: A:K.216 SO4.8: 4 residues within 4Å: Chain A: V.221, L.241, K.242, H.243 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.243, A:N.244 SO4.9: 2 residues within 4Å: Chain A: R.57, H.157 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.157 Salt bridges: A:R.57, A:H.157 SO4.10: 2 residues within 4Å: Chain A: R.28, K.33 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.28, A:K.33 SO4.11: 2 residues within 4Å: Chain A: E.52 Ligands: T3I.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.47 Water bridges: A:R.56 SO4.12: 3 residues within 4Å: Chain A: R.56, Y.76, H.78 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.76 Salt bridges: A:R.56, A:H.78 SO4.13: 2 residues within 4Å: Chain A: H.53, R.57 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Q.54 Salt bridges: A:H.53, A:R.57

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

DMS.14: 4 residues within 4Å: Chain A: S.122, M.250, L.251, R.252 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.251 DMS.15: 4 residues within 4Å: Chain A: L.7, Y.25, R.82, Y.84 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:Y.25

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

ACT.16: 3 residues within 4Å: Chain A: R.181, H.243, N.244 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.243

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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