SMTL ID : 6t41.1

CDK8/Cyclin C in complex with N-(4-chlorobenzyl)isoquinolin-4-amine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

hetero-1-1-mer

Ligands

1 x MFE: ~{N}-[(4-chlorophenyl)methyl]quinazolin-4-amine(Non-covalent)

MFE.1: 17 residues within 4Å: Chain A: V.30, G.31, V.38, A.53, K.55, I.82, F.100, D.101, Y.102, A.103, D.106, W.108, H.109, A.158, L.161, A.175, R.359 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.53, A:I.82, A:I.82, A:F.100, A:F.100, A:L.161 Hydrogen bonds: A:A.103 pi-Cation interactions: A:R.359

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

EDO.2: 8 residues within 4Å: Chain A: D.5, D.7, F.8 Chain B: K.30, Y.79, S.80, K.82, S.83 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.80, A:D.5, A:F.8

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

FMT.3: 6 residues within 4Å: Chain A: R.74, E.75 Chain B: Q.10, S.11, S.12, L.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.74 Water bridges: A:R.74 FMT.4: 4 residues within 4Å: Chain A: R.74, K.86, V.87 Chain B: D.150 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.74, A:V.87 FMT.5: 5 residues within 4Å: Chain B: F.8, Y.156, P.161, P.197, F.198 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.198 FMT.6: 7 residues within 4Å: Chain B: T.48, N.49, N.184, D.185, R.188, W.244 Ligands: FMT.7 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.181 FMT.7: 9 residues within 4Å: Chain B: T.48, Q.52, Q.62, I.65, A.66, Y.159, N.184, Y.187 Ligands: FMT.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.62, B:N.184

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Klatt, F. et al., A precisely positioned MED12 activation helix stimulates CDK8 kinase activity. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-01-01

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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