SMTL ID : 4f6w.1

Crystal structure of human CDK8/CYCC in complex with compound 1 (N-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]-4-[2-({[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]carbamoyl}amino)ethyl]piperazine-1-carboxamide)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 0SS: N-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]-4-[2-({[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]carbamoyl}amino)ethyl]piperazine-1-carboxamide(Non-covalent)

0SS.1: 22 residues within 4Å: Chain A: V.29, Y.34, V.37, S.64, E.68, L.72, L.75, V.80, I.81, F.99, Y.101, W.107, H.108, H.151, L.160, I.173, A.174, D.175, M.176, G.177, R.358 Ligands: DMS.2 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:V.37, A:E.68, A:L.75, A:V.80, A:I.81, A:Y.101, A:W.107, A:L.160, A:I.173, A:D.175 Hydrogen bonds: A:E.68, A:E.68, A:D.175 Water bridges: A:Y.34, A:D.175 pi-Cation interactions: A:R.358

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 3 residues within 4Å: Chain A: K.155, A.157 Ligands: 0SS.1 No protein-ligand interaction detected (PLIP)

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

EDO.3: 4 residues within 4Å: Chain A: Y.135, Q.136, T.344, S.345 No protein-ligand interaction detected (PLIP) EDO.4: 3 residues within 4Å: Chain A: K.309, P.335, L.338 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.309, A:P.335 EDO.5: 3 residues within 4Å: Chain A: P.126, G.128, M.129 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.128, A:M.129 EDO.6: 7 residues within 4Å: Chain A: R.15, E.16, K.85, V.86, F.87, L.88 Ligands: FMT.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.16, A:K.85, A:L.88 EDO.9: 5 residues within 4Å: Chain B: A.4, M.5, A.6, V.156, Y.157 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.4, B:V.156 Water bridges: B:V.156 EDO.10: 4 residues within 4Å: Chain B: Q.53, E.57, L.61, Q.63 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.53, B:G.56, B:L.61, B:Q.63 EDO.11: 3 residues within 4Å: Chain B: Q.165, Y.166, F.199 No protein-ligand interaction detected (PLIP) EDO.12: 5 residues within 4Å: Chain A: L.11 Chain B: Y.80, Y.145, E.148, L.149 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.149 EDO.13: 5 residues within 4Å: Chain A: T.59, I.61 Chain B: F.96, K.100, V.106 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.100, B:K.100

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

FMT.7: 4 residues within 4Å: Chain A: K.85, V.86 Chain B: D.151 Ligands: EDO.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.86, A:V.86 FMT.8: 5 residues within 4Å: Chain A: E.19, F.22, E.23, Y.24, E.25 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.24, A:E.25 FMT.14: 4 residues within 4Å: Chain B: N.50, R.189, F.248, E.250 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.50, B:R.189, B:R.189 FMT.15: 6 residues within 4Å: Chain B: Q.45, T.49, T.70, F.73, K.74, Y.188 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.49, B:K.74 FMT.16: 6 residues within 4Å: Chain B: K.121, T.122, R.123, F.124, S.125, R.251 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.125, B:S.125, B:R.251

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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