SMTL ID : 3fc2.1

PLK1 in complex with BI6727

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-dimer

Ligands

2 x IBI: N-{trans-4-[4-(cyclopropylmethyl)piperazin-1-yl]cyclohexyl}-4-{[(7R)-7-ethyl-5-methyl-8-(1-methylethyl)-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxybenzamide(Non-covalent)

IBI.1: 16 residues within 4Å: Chain A: R.47, F.48, L.49, C.57, E.59, A.70, V.104, L.120, E.121, L.122, C.123, R.124, R.126, F.173 Ligands: EDO.3, GOL.10 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.49, A:A.70, A:R.126, A:F.173 Hydrogen bonds: A:R.47, A:L.49, A:C.123, A:C.123 Water bridges: A:D.184 IBI.11: 16 residues within 4Å: Chain B: R.47, F.48, L.49, C.57, E.59, A.70, V.104, L.120, E.121, L.122, C.123, R.124, R.126, F.173 Ligands: EDO.13, GOL.20 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.49, B:A.70, B:R.126, B:F.173 Hydrogen bonds: B:R.47, B:L.49, B:C.123, B:C.123 Water bridges: B:D.184

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 4 residues within 4Å: Chain A: R.125, R.126, E.130, L.309 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.131 EDO.3: 6 residues within 4Å: Chain A: K.168, G.170, N.171, D.184 Ligands: IBI.1, GOL.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.168, A:K.168 EDO.5: 4 residues within 4Å: Chain A: H.100, L.152, Q.155, Y.156 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.152, A:Q.155, A:Y.156 EDO.7: 3 residues within 4Å: Chain A: N.206, Y.207, P.239 No protein-ligand interaction detected (PLIP) EDO.12: 4 residues within 4Å: Chain B: R.125, R.126, E.130, L.309 1 PLIP interactions: 1 interactions with chain B Water bridges: B:L.131 EDO.13: 6 residues within 4Å: Chain B: K.168, G.170, N.171, D.184 Ligands: IBI.11, GOL.20 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.168, B:K.168, B:D.184 EDO.15: 4 residues within 4Å: Chain B: H.100, L.152, Q.155, Y.156 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.152, B:Q.155, B:Y.156 EDO.17: 3 residues within 4Å: Chain B: N.206, Y.207, P.239 No protein-ligand interaction detected (PLIP)

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

ACT.4: 4 residues within 4Å: Chain A: F.54, K.72, M.88, E.91 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.54, A:E.91 Salt bridges: A:K.72 ACT.8: 7 residues within 4Å: Chain A: H.83, Q.84, K.87, C.202 Chain B: C.245, L.246 Ligands: ZN.9 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.84, B:L.246 Salt bridges: A:H.83, A:K.87 Hydrophobic interactions: B:L.246 ACT.14: 4 residues within 4Å: Chain B: F.54, K.72, M.88, E.91 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.54, B:E.91 Salt bridges: B:K.72 ACT.18: 7 residues within 4Å: Chain A: C.245, L.246 Chain B: H.83, Q.84, K.87, C.202 Ligands: ZN.19 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.84, A:L.246 Salt bridges: B:H.83, B:K.87 Hydrophobic interactions: A:L.246

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 3 residues within 4Å: Chain A: Y.156, R.159, N.160 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.160 PEG.16: 3 residues within 4Å: Chain B: Y.156, R.159, N.160 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.160

2 x ZN: ZINC ION(Non-covalent)

ZN.9: 6 residues within 4Å: Chain A: H.83, K.87, C.202 Chain B: C.245, L.246 Ligands: ACT.8 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: A:H.83, A:C.202, B:C.245, ACT.8 ZN.19: 6 residues within 4Å: Chain A: C.245, L.246 Chain B: H.83, K.87, C.202 Ligands: ACT.18 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: B:H.83, B:C.202, A:C.245, ACT.18

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 7 residues within 4Å: Chain A: R.126, S.127, E.130, G.170, F.173 Ligands: IBI.1, EDO.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.126, A:R.126, A:G.170 GOL.20: 7 residues within 4Å: Chain B: R.126, S.127, E.130, G.170, F.173 Ligands: IBI.11, EDO.13 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.126, B:R.126, B:G.170

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rudolph, D. et al., BI 6727, A Polo-like Kinase Inhibitor with Improved Pharmacokinetic Profile and Broad Antitumor Activity. Clin.Cancer Res. (2009)

Release Date

2009-05-12

Peptides

Serine/threonine-protein kinase PLK1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Serine/threonine-protein kinase PLK1

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