SMTL ID : 5cei.1

Crystal structure of CDK8:Cyclin C complex with compound 22

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.24 Å

Oligo State

hetero-1-1-mer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: R.74, E.75 Chain B: Q.11, S.13, Q.17 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.74, A:E.75, B:Q.17 EDO.2: 3 residues within 4Å: Chain A: H.143, Y.144, A.147 2 PLIP interactions: 2 interactions with chain A Water bridges: A:H.78, A:H.143 EDO.3: 6 residues within 4Å: Chain A: E.20, F.23, E.24, Y.25, E.26, K.44 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.20, A:E.24, A:Y.25, A:E.26, A:K.44 EDO.4: 4 residues within 4Å: Chain A: K.304, V.305, K.306, S.309 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.306 EDO.9: 3 residues within 4Å: Chain A: P.307, D.308, H.313 No protein-ligand interaction detected (PLIP) EDO.10: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain B Water bridges: B:W.10 EDO.11: 4 residues within 4Å: Chain B: E.39, E.243, Q.244, N.247 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.243, B:Q.244 EDO.16: 5 residues within 4Å: Chain B: I.46, N.50, W.245, F.248, E.250 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.50, B:F.248, B:E.250

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

FMT.5: 8 residues within 4Å: Chain A: K.55, E.69, L.73, I.82, F.100, A.175, D.176 Ligands: 50R.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.55, A:D.176 FMT.6: 3 residues within 4Å: Chain A: E.168, R.169, R.171 No protein-ligand interaction detected (PLIP) FMT.7: 4 residues within 4Å: Chain A: N.80, Q.137, R.171, S.346 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.80, A:R.171 Water bridges: A:N.80 FMT.12: 6 residues within 4Å: Chain B: A.4, A.6, I.155, V.156, Y.157, R.161 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.161 FMT.13: 4 residues within 4Å: Chain B: F.35, S.259, K.260, M.261 1 PLIP interactions: 1 interactions with chain B Water bridges: B:M.261 FMT.14: 2 residues within 4Å: Chain B: R.62, Q.63 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.63 Water bridges: B:Q.64 FMT.15: 4 residues within 4Å: Chain B: Q.53, E.57, L.61, Q.63 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.53, B:L.61

1 x 50R: 4-(4-iodophenoxy)-N-methylthieno[2,3-c]pyridine-2-carboxamide(Non-covalent)

50R.8: 16 residues within 4Å: Chain A: V.30, Y.35, V.38, A.53, K.55, I.82, D.101, Y.102, A.103, D.106, H.109, A.158, L.161, D.176, R.359 Ligands: FMT.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.38, A:L.161, A:L.161 Hydrogen bonds: A:A.103 Water bridges: A:Y.35 pi-Cation interactions: A:R.359

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koehler, M.F. et al., Development of a Potent, Specific CDK8 Kinase Inhibitor Which Phenocopies CDK8/19 Knockout Cells. Acs Med.Chem.Lett. (2016)

Release Date

2016-02-10

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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