SMTL ID : 6r4a.1

Aurora-A in complex with shape-diverse fragment 55

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

monomer

Ligands

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

ADP.1: 19 residues within 4Å: Chain A: L.21, G.22, G.24, K.25, F.26, G.27, V.29, A.42, K.44, L.76, E.93, A.95, T.99, E.142, N.143, L.145, D.156 Ligands: MG.4, MG.5 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:K.25, A:F.26, A:G.27, A:E.93, A:A.95 Water bridges: A:K.23, A:K.44, A:E.142, A:E.142, A:N.143 Salt bridges: A:K.44, A:K.44

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: V.161, H.162, P.164, S.165 Ligands: CL.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.162 GOL.3: 5 residues within 4Å: Chain A: Y.101, G.207, K.208, P.209, E.212 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.101, A:Y.101, A:E.212

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: N.143, D.156 Ligands: ADP.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.156, H2O.3, H2O.3 MG.5: 3 residues within 4Å: Chain A: K.44, D.156 Ligands: ADP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.156, H2O.1, H2O.4, H2O.4

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

CL.6: 4 residues within 4Å: Chain A: S.165, S.166, R.168 Ligands: GOL.2 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: R.137, R.167, R.168, T.169 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: M.255, L.256, R.257 Ligand excluded by PLIP CL.9: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

1 x JRT: 2-(benzimidazol-1-yl)-~{N}-(2-phenylethyl)ethanamide(Non-covalent)

JRT.10: 8 residues within 4Å: Chain A: E.57, L.60, R.61, V.64, E.65, Y.81, H.83, V.88 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.60, A:L.60, A:R.61, A:R.61, A:Y.81 Hydrogen bonds: A:R.61 pi-Cation interactions: A:R.61

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, R. et al., Construction of a Shape-Diverse Fragment Set: Design, Synthesis and Screen against Aurora-A Kinase. Chemistry (2019)

Release Date

2019-05-08

Peptides

Aurora kinase A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Aurora kinase A

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