SMTL ID : 8c1h.1

Aurora A kinase in complex with TPX2-inhibitor 8

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.23 Å

Oligo State

monomer

Ligands

1 x T3U: 4-(4-chloranyl-3-pyrazin-2-yloxy-phenyl)-~{N}-(dimethylsulfamoyl)-7-methyl-1~{H}-indole-6-carboxamide

T3U.1: 14 residues within 4Å: Chain A: K.43, L.46, E.47, E.52, L.55, R.56, V.59, Y.76, F.77, H.78, A.80, V.83 Ligands: SO4.10, CL.14 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:V.83 Hydrogen bonds: A:K.43, A:K.43, A:E.47, A:E.47, A:R.56, A:R.56 pi-Cation interactions: A:K.43, A:R.56, A:H.78

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.5 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:K.20, A:E.88, A:A.90 Water bridges: A:G.93, A:E.137, A:E.137, A:N.138, A:N.138, A:D.151, A:D.151, 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.1, H2O.2 MG.4: 5 residues within 4Å: Chain A: K.39, D.151 Ligands: ADP.2, MG.3, T5L.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.151, A:D.151, H2O.1, H2O.1

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

T5L.5: 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 11 PLIP interactions: 11 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:D.133, A:W.154 Salt bridges: A:K.39, A:K.39

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

SO4.6: 1 residues within 4Å: Chain A: Q.212 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.216 SO4.7: 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 SO4.8: 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 SO4.9: 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 SO4.10: 2 residues within 4Å: Chain A: E.52 Ligands: T3U.1 No protein-ligand interaction detected (PLIP)

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

DMS.11: 4 residues within 4Å: Chain A: S.122, M.250, L.251, R.252 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.251, A:R.252 DMS.12: 2 residues within 4Å: Chain A: Y.25, R.82 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.25

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

ACT.13: 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

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

CL.14: 2 residues within 4Å: Chain A: H.78 Ligands: T3U.1 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain A: H.53, R.57 Ligand excluded by PLIP

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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