SMTL ID : 5fgk.1

CDK8-CYCC IN COMPLEX WITH 8-[3-(3-Amino-1H-indazol-6-yl)-5-chloro- pyridine-4-yl]-2,8-diaza-spiro[4.5]decan-1-one

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.36 Å

Oligo State

hetero-oligomer

Ligands

1 x 5XG: 8-[3-(3-azanyl-2~{H}-indazol-6-yl)-5-chloranyl-pyridin-4-yl]-2,8-diazaspiro[4.5]decan-1-one(Non-covalent)

5XG.1: 16 residues within 4Å: Chain A: V.29, G.30, Y.34, V.37, A.52, K.54, I.81, F.99, D.100, Y.101, A.102, D.105, L.160, D.175, R.358 Ligands: DMS.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.29, A:Y.34 Hydrogen bonds: A:V.29, A:K.54, A:A.102, A:D.175 Water bridges: A:Y.34, A:R.358, A:R.358 pi-Cation interactions: A:R.358, A:R.358

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

DMS.2: 10 residues within 4Å: Chain A: K.54, E.68, L.72, I.81, F.99, A.174, D.175, M.176, F.178 Ligands: 5XG.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.175, A:M.176 Salt bridges: A:E.68

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

EDO.3: 4 residues within 4Å: Chain A: P.126, R.127, G.128, M.129 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.127, A:G.128 EDO.10: 5 residues within 4Å: Chain A: R.152, D.153, G.177, R.202, Y.213 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.202, A:R.202, A:Y.213

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

FMT.4: 5 residues within 4Å: Chain A: Q.124, R.127, L.230, T.231, H.302 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.124, A:R.127, A:T.231 FMT.5: 4 residues within 4Å: Chain A: R.127, V.304, K.305, S.308 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.127, A:K.305, A:S.308 FMT.6: 4 residues within 4Å: Chain A: H.145, A.146, W.148, K.215 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.215 Water bridges: A:K.215 FMT.7: 3 residues within 4Å: Chain A: D.255, R.256, N.259 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.256, A:N.259 FMT.8: 8 residues within 4Å: Chain A: I.56, E.57, G.58, T.59, G.60, S.62, A.65, V.95 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.62 FMT.9: 6 residues within 4Å: Chain A: E.19, F.22, E.23, Y.24, E.25, K.43 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.24, A:E.25, A:K.43 FMT.11: 6 residues within 4Å: Chain B: Q.43, T.47, T.68, F.71, K.72, Y.186 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.47, B:K.72 Water bridges: B:Q.43

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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