SMTL ID : 5hbe.1

CDK8-CYCC IN COMPLEX WITH 8-[3-Chloro-5-(1-methyl-2,2-dioxo-2, 3-dihydro-1H-2l6-benzo[c]isothiazol-5-yl)-pyridin- 4-yl]-1-oxa-3,8-diaza-spiro[4.5]decan-2-one

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 5Y6: 8-[3-chloranyl-5-[1-methyl-2,2-bis(oxidanylidene)-3~{H}-2,1-benzothiazol-5-yl]pyridin-4-yl]-1-oxa-3,8-diazaspiro[4.5]decan-2-one(Non-covalent)

5Y6.1: 18 residues within 4Å: Chain A: V.29, Y.34, V.37, A.52, K.54, I.81, F.99, D.100, Y.101, A.102, D.105, H.108, A.157, L.160, A.174, D.175, R.358 Ligands: DMS.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.37, A:L.160, A:A.174 Hydrogen bonds: A:A.102, A:D.175 Water bridges: A:Y.34, A:D.175 pi-Cation interactions: A:R.358

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

DMS.2: 9 residues within 4Å: Chain A: K.54, E.68, L.72, I.81, F.99, A.174, D.175, F.178 Ligands: 5Y6.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.175 Salt bridges: A:E.68

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

EDO.3: 5 residues within 4Å: Chain A: H.77, P.78, V.80, S.82, K.172 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.80 Water bridges: A:H.77

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

FMT.4: 6 residues within 4Å: Chain A: Q.124, P.126, R.127, G.128, M.129, V.130 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.124, A:G.128, A:M.129, A:V.130 FMT.5: 5 residues within 4Å: Chain B: Q.51, Q.61, A.65, Y.158, Y.186 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.61 FMT.6: 7 residues within 4Å: Chain B: K.119, T.120, R.121, F.122, S.123, Y.124, R.249 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.119, B:S.123, B:R.249 FMT.7: 4 residues within 4Å: Chain B: Q.15, R.77, L.147, D.149 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.15, B:R.77, B:L.147 Water bridges: B:R.77, B:R.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mallinger, A. et al., Discovery of Potent, Selective, and Orally Bioavailable Small-Molecule Modulators of the Mediator Complex-Associated Kinases CDK8 and CDK19. J.Med.Chem. (2016)

Release Date

2016-02-03

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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