SMTL ID : 8c1f.1

Aurora A kinase in complex with TPX2-inhibitor 6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

monomer

Ligands

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

ADP.1: 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.2, MG.3, T5L.9 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:K.20, A:E.88, A:A.90, A:D.151 Water bridges: A:K.18, A:K.18, A:F.21, A:E.137, A:N.138, A:N.138, A:N.138, A:N.138, A:N.138, A:D.151, A:G.153 Salt bridges: A:K.20, A:K.39, A:K.39

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: N.138, D.151 Ligands: ADP.1, MG.3 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.151, H2O.1, H2O.2 MG.3: 4 residues within 4Å: Chain A: D.151 Ligands: ADP.1, MG.2, T5L.9 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.151, A:D.151, H2O.1, H2O.2

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: H.78, D.79 Ligands: T2O.17 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.78 Water bridges: A:R.3, A:H.78 GOL.5: 4 residues within 4Å: Chain A: S.122, M.250, L.251, R.252 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.122, A:S.122, A:L.251, A:R.252 GOL.6: 5 residues within 4Å: Chain A: A.6, L.7, E.8, D.79 Ligands: GOL.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.7, A:E.8, A:E.8, A:D.79 GOL.7: 5 residues within 4Å: Chain A: E.107, T.230, G.232, W.259, N.263 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.107, A:G.232 GOL.8: 5 residues within 4Å: Chain A: D.79, A.80, T.81, R.82 Ligands: GOL.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.80, A:T.81, A:T.81, A:R.82

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

T5L.9: 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.1, MG.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.21, A:F.21, A:V.51, A:V.51, A:Q.54, A:L.55, A:W.154 Hydrogen bonds: A:E.58 Water bridges: A:F.21, A:W.154 Salt bridges: A:K.39, A:K.39

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

SO4.10: 2 residues within 4Å: Chain A: Q.212, K.216 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.216 SO4.11: 5 residues within 4Å: Chain A: V.221, L.241, K.242, H.243, N.244 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.243, A:N.244 SO4.12: 3 residues within 4Å: Chain A: R.57, V.156, H.157 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.157 Salt bridges: A:R.57, A:H.157 SO4.13: 1 residues within 4Å: Chain A: R.28 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.28 SO4.14: 2 residues within 4Å: Chain A: E.52 Ligands: T2O.17 No protein-ligand interaction detected (PLIP) SO4.15: 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

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

DMS.16: 4 residues within 4Å: Chain A: L.7, V.40, R.82, Y.84 No protein-ligand interaction detected (PLIP)

1 x T2O: 4-(4-chlorophenyl)-~{N}-cyclopropylsulfonyl-7-methyl-1~{H}-indole-6-carboxamide

T2O.17: 13 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: GOL.4, SO4.14 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:K.43, A:L.46, A:E.52, A:L.55, A:Y.76, A:V.83, A:V.83 Hydrogen bonds: A:K.43, A:K.43, A:E.47, A:E.47 pi-Stacking: A:H.78 pi-Cation interactions: A:K.43

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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