SMTL ID : 4f6s.1

Crystal structure of human CDK8/CYCC in complex with compound 7 (1-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]urea)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 0SQ: 1-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]urea(Non-covalent)

0SQ.1: 13 residues within 4Å: Chain A: Y.34, K.54, S.64, R.67, E.68, L.75, I.81, F.99, H.151, I.173, A.174, D.175 Ligands: FMT.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.34, A:E.68, A:L.75, A:I.81, A:I.173 Hydrogen bonds: A:K.54, A:K.54, A:E.68, A:D.175, A:D.175

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

EDO.2: 6 residues within 4Å: Chain A: V.37, A.52, I.81, D.100, A.102, L.160 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.100, A:A.102 EDO.7: 5 residues within 4Å: Chain B: Y.41, Q.45, K.74, D.191 Ligands: FMT.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.191 EDO.8: 5 residues within 4Å: Chain B: Q.64, Y.157, H.158, Y.160, R.161 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.158, B:Y.160, B:R.161 EDO.9: 5 residues within 4Å: Chain B: A.4, E.102, I.155, V.156, Y.157 1 PLIP interactions: 1 interactions with chain B Water bridges: B:V.156

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

FMT.3: 3 residues within 4Å: Chain A: R.152, H.212, Y.213 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.152, A:Y.213 FMT.4: 5 residues within 4Å: Chain A: Y.34, S.64, R.67, R.152 Ligands: 0SQ.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.64, A:R.67, A:R.152 FMT.5: 4 residues within 4Å: Chain A: R.73, E.74 Chain B: Q.11, S.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.73 FMT.6: 5 residues within 4Å: Chain A: I.81, S.82, D.100, E.167, K.172 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.82, A:D.100, A:D.100 FMT.10: 7 residues within 4Å: Chain B: Q.45, T.49, T.70, F.73, K.74, Y.188 Ligands: EDO.7 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.49, B:K.74 FMT.11: 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.12: 4 residues within 4Å: Chain B: F.9, P.162, P.198, F.199 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.199

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schneider, E.V. et al., Structure-kinetic relationship study of CDK8/CycC specific compounds. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2013-05-01

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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