SMTL ID : 5idp.1

CDK8-CYCC IN COMPLEX WITH (3-Amino-1H-indazol-5-yl)-[(S)-2-(4-fluoro-phenyl)-piperidin-1-yl]-methanone

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 6A6: (3-amino-1H-indazol-5-yl)[(2S)-2-(4-fluorophenyl)piperidin-1-yl]methanone(Non-covalent)

6A6.1: 18 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 Ligands: FMT.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.34, A:V.37, A:A.52, A:F.99, A:N.158, A:L.160, A:L.160, A:D.175 Hydrogen bonds: A:D.100, A:A.102, A:A.102, A:R.358

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

FMT.2: 5 residues within 4Å: Chain A: E.68, F.99, A.174, D.175 Ligands: 6A6.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.175 FMT.3: 4 residues within 4Å: Chain A: R.73, K.85, V.86 Chain B: D.151 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.73, A:V.86 FMT.4: 5 residues within 4Å: Chain B: Q.45, T.49, T.70, F.73, K.74 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.49, B:K.74 FMT.5: 6 residues within 4Å: Chain B: Q.53, Q.63, A.67, T.70, Y.160, Y.188 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.63, B:Y.160 FMT.6: 5 residues within 4Å: Chain B: D.2, A.4, M.5, A.6, Y.157 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.2, B:R.161

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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