SMTL ID : 4f6u.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-mer

Ligands

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

0SR.1: 22 residues within 4Å: Chain A: Y.34, V.37, A.52, K.54, S.64, R.67, E.68, L.72, L.75, V.80, I.81, F.99, D.100, Y.101, A.102, H.151, L.160, I.173, A.174, D.175, M.176 Ligands: FMT.11 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.34, A:Y.34, A:E.68, A:L.75, A:V.80, A:I.81, A:F.99, A:I.173 Hydrogen bonds: A:E.68, A:E.68, A:A.102, A:D.175 Water bridges: A:D.175

1 x NA: SODIUM ION(Non-functional Binders)

NA.2: 4 residues within 4Å: Chain A: H.77, D.139, H.142, Y.143 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.139, A:D.139

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

DMS.3: 6 residues within 4Å: Chain A: P.166, E.167, R.168, R.170, S.345, D.346 No protein-ligand interaction detected (PLIP)

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

EDO.4: 6 residues within 4Å: Chain A: R.73, E.74 Chain B: Q.11, S.13, L.16, Q.17 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:N.8 Hydrogen bonds: A:R.73, A:R.73, A:E.74 EDO.5: 6 residues within 4Å: Chain A: H.251, D.255, D.284, F.285, T.289, Y.290 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.255, A:D.255, A:D.284, A:T.289 EDO.6: 4 residues within 4Å: Chain A: L.72, R.73, L.83 Ligands: EDO.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.73 Water bridges: A:L.75 EDO.7: 5 residues within 4Å: Chain A: R.73, 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 EDO.8: 5 residues within 4Å: Chain A: P.126, R.127, G.128, M.129, A.349 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.127, A:G.128, A:M.129 Water bridges: A:F.348 EDO.9: 8 residues within 4Å: Chain A: V.18, E.19, Y.24, Q.55, S.89, D.92, K.94, W.96 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.24, A:S.89, A:D.92 EDO.12: 7 residues within 4Å: Chain B: K.3, A.4, M.5, A.6, I.155, V.156, Y.157 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.4, B:V.156 EDO.13: 6 residues within 4Å: Chain B: I.46, N.50, R.189, W.245, F.248, E.250 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.50, B:R.189, B:R.189, B:W.245 Water bridges: B:E.250 EDO.14: 2 residues within 4Å: Chain B: Q.165, Y.166 No protein-ligand interaction detected (PLIP) EDO.15: 4 residues within 4Å: Chain B: W.42, E.243, Q.244, N.247 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.247

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

FMT.10: 4 residues within 4Å: Chain A: Y.135, P.343, T.344, S.345 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.343 FMT.11: 3 residues within 4Å: Chain A: Y.34, R.67 Ligands: 0SR.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.34, A:R.67 Water bridges: A:D.175 FMT.16: 7 residues within 4Å: Chain B: Q.45, T.49, T.70, F.73, K.74, Y.188 Ligands: FMT.18 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.49, B:K.74 FMT.17: 3 residues within 4Å: Chain B: H.58, L.59, R.111 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.58, B:R.111 FMT.18: 5 residues within 4Å: Chain B: Y.41, Q.45, F.73, Y.77 Ligands: FMT.16 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.45 FMT.19: 5 residues within 4Å: Chain B: V.88, F.128, K.130, E.131, P.133 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.130

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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