SMTL ID : 5icp.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 69Z: [(2S)-2-(4-chlorophenyl)pyrrolidin-1-yl](5-methylimidazo[5,1-b][1,3,4]thiadiazol-2-yl)methanone(Non-covalent)

69Z.1: 16 residues within 4Å: Chain A: V.29, G.30, Y.34, V.37, A.52, K.54, F.99, D.100, Y.101, A.102, A.157, N.158, L.160, D.175, R.358 Ligands: EDO.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.34, A:V.37, A:V.37, A:L.160, A:D.175 Hydrogen bonds: A:K.54, A:A.102 Halogen bonds: A:V.29

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

EDO.2: 5 residues within 4Å: Chain A: H.108, P.356, K.357, R.358, E.359 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.356, A:E.359 Water bridges: A:R.358, A:E.359 EDO.3: 4 residues within 4Å: Chain A: R.73, K.85, V.86 Chain B: D.150 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.73, A:V.86, A:V.86 EDO.4: 9 residues within 4Å: Chain A: K.54, E.68, L.72, I.81, F.99, A.174, D.175, F.178 Ligands: 69Z.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.54, A:D.175 Water bridges: A:D.175

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

FMT.5: 4 residues within 4Å: Chain A: R.73, E.74 Chain B: Q.10, S.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.73 FMT.6: 6 residues within 4Å: Chain A: P.264, D.266, I.272, H.278, M.282, R.287 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.278, A:R.287 FMT.7: 6 residues within 4Å: Chain A: E.19, F.22, E.23, Y.24, E.25, K.43 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.24, A:E.25, A:K.43 Water bridges: A:E.25, A:E.25 FMT.8: 7 residues within 4Å: Chain B: A.3, M.4, A.5, I.154, V.155, Y.156, R.160 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.63, B:R.160 FMT.9: 3 residues within 4Å: Chain B: Q.44, F.72 Ligands: FMT.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.44 FMT.10: 7 residues within 4Å: Chain B: Q.44, T.48, T.69, F.72, K.73, Y.187 Ligands: FMT.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.48, B:K.73 FMT.11: 5 residues within 4Å: Chain B: H.206, K.214, D.215, A.216, F.220 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.206, B:A.216 FMT.12: 3 residues within 4Å: Chain B: F.8, P.197, F.198 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.198 FMT.13: 7 residues within 4Å: Chain B: Q.52, Q.62, A.66, T.69, Y.159, Y.187, R.188 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.62, B:Y.159, B:R.188 Water bridges: B:Q.52

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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