SMTL ID : 6tpa.1

CDK8/CyclinC in complex with drug ETP-50775

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NZ8: 1-[4-chloranyl-3-(trifluoromethyl)phenyl]-3-(5-oxidanylidene-6-pyridin-4-yl-pyrido[2,3-b][1,5]benzoxazepin-9-yl)urea(Non-covalent)

NZ8.1: 22 residues within 4Å: Chain A: Y.34, V.37, A.52, K.54, E.68, L.72, L.75, V.80, I.81, F.99, D.100, Y.101, A.102, L.144, V.149, H.151, I.173, A.174, D.175, M.176, F.178, R.358 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.34, A:V.37, A:A.52, A:E.68, A:L.72, A:I.81, A:F.99, A:A.174, A:D.175, A:M.176, A:F.178 Hydrogen bonds: A:E.68, A:E.68, A:E.68, A:A.102, A:D.175 Halogen bonds: A:I.173

12 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 3 residues within 4Å: Chain A: L.72, L.75, S.82 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.82 FMT.3: 3 residues within 4Å: Chain A: L.150, R.152 Chain B: E.101 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:L.150, A:R.152, B:E.101 FMT.4: 1 residues within 4Å: Ligands: NZ5.5 No protein-ligand interaction detected (PLIP) FMT.8: 2 residues within 4Å: Chain B: K.228, E.231 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.228 FMT.9: 3 residues within 4Å: Chain B: S.11, L.14, Q.15 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.73, B:Q.15 FMT.10: 4 residues within 4Å: Chain B: K.20, D.189, L.193, V.235 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.20 Water bridges: B:D.189 FMT.11: 3 residues within 4Å: Chain B: N.48, N.183, D.184 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.184 FMT.12: 1 residues within 4Å: Chain B: L.175 No protein-ligand interaction detected (PLIP) FMT.13: 4 residues within 4Å: Chain B: A.2, A.4, I.153, V.154 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.154 FMT.14: 1 residues within 4Å: Chain B: I.17 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.19 FMT.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) FMT.16: 2 residues within 4Å: Chain B: V.209, Q.212 No protein-ligand interaction detected (PLIP)

4 x NZ5: (2~{R})-butane-1,2-diol(Non-covalent)

NZ5.5: 2 residues within 4Å: Chain A: Q.84 Ligands: FMT.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.84 Water bridges: A:R.73 NZ5.6: 2 residues within 4Å: Chain A: P.343, S.345 No protein-ligand interaction detected (PLIP) NZ5.7: 5 residues within 4Å: Chain A: R.127, K.131, A.310, Y.336, E.339 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.127 Hydrogen bonds: A:A.310 NZ5.17: 2 residues within 4Å: Chain B: L.177, R.180 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.177, B:R.180 Hydrogen bonds: B:R.180

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Martinez-Gonzalez, S. et al., Pyrido[2,3-b][1,5]benzoxazepin-5(6H)-one derivatives as CDK8 inhibitors. Eur.J.Med.Chem. (2020)

Release Date

2020-11-18

Peptides

Cyclin-dependent kinase 8: A
Cyclin-C: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cyclin-dependent kinase 8

Cyclin-C

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