SMTL ID : 5idn.1

CDK8-CYCC IN COMPLEX WITH [(S)-2-(4-Chloro-phenyl)-pyrrolidin-1-yl]-(3-methyl-1H-pyrazolo[3,4-b]pyridin-5-yl)-methanone

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.26 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 6A7: [(2S)-2-(4-chlorophenyl)pyrrolidin-1-yl](3-methyl-1H-pyrazolo[3,4-b]pyridin-5-yl)methanone(Non-covalent)

6A7.1: 17 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, A.157, N.158, L.160, D.175, R.358 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.34, A:Y.34, A:V.37, A:A.52, A:N.158, A:L.160, A:L.160, A:D.175 Hydrogen bonds: A:K.54, A:D.100, A:A.102 Halogen bonds: A:V.29

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

EDO.2: 5 residues within 4Å: Chain A: R.127, L.230, 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

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

FMT.3: 5 residues within 4Å: Chain A: H.151, D.153, N.158, D.175, F.178 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.153, A:N.158 Water bridges: A:K.155, A:K.155, A:F.178 FMT.4: 5 residues within 4Å: Chain A: Y.34, K.54, S.64, A.65, E.68 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.34 FMT.5: 6 residues within 4Å: Chain A: V.18, E.19, Y.24, S.89, D.92, W.96 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.89, A:D.92 FMT.6: 5 residues within 4Å: Chain B: A.5, G.6, Y.156, R.160 Ligands: FMT.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.6, B:R.160 Water bridges: B:H.157, B:H.157 FMT.7: 4 residues within 4Å: Chain B: A.3, V.155, Y.156 Ligands: FMT.6 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.160 FMT.8: 6 residues within 4Å: Chain B: H.206, C.209, K.214, D.215, A.216, R.217 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.214, B:A.216

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Czodrowski, P. et al., Structure-Based Optimization of Potent, Selective, and Orally Bioavailable CDK8 Inhibitors Discovered by High-Throughput Screening. J. Med. Chem. (2016)

Release Date

2016-12-21

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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