SMTL ID : 5hnb.1

CDK8-CYCC IN COMPLEX WITH [6-Hydroxy-3-(3-methyl-benzyl)-1H-indazol-5-yl]-((S)-3-hydroxy-pyrrolidin-1-yl)-methanone

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 62M: [6-hydroxy-3-(3-methylbenzyl)-1H-indazol-5-yl][(3S)-3-hydroxypyrrolidin-1-yl]methanone(Non-covalent)

62M.1: 18 residues within 4Å: Chain A: V.30, G.31, Y.35, V.38, A.53, K.55, I.82, F.100, D.101, Y.102, A.103, D.106, A.158, N.159, L.161, D.176, R.359 Ligands: FMT.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.30, A:Y.35, A:A.53, A:I.82, A:F.100, A:Y.102, A:L.161, A:L.161 Hydrogen bonds: A:D.101, A:A.103, A:N.159, A:D.176 pi-Cation interactions: A:R.359

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

FMT.2: 7 residues within 4Å: Chain A: E.69, L.73, I.82, F.100, D.176, F.179 Ligands: 62M.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.69, A:D.176 FMT.3: 4 residues within 4Å: Chain A: R.153, Y.202, Y.214, I.218 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.202 Water bridges: A:R.153, A:L.155 FMT.4: 4 residues within 4Å: Chain A: R.74, E.75 Chain B: Q.9, S.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.74, A:E.75 FMT.5: 4 residues within 4Å: Chain A: P.167, E.168, R.169, R.171 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.169 FMT.6: 2 residues within 4Å: Chain A: V.305, K.306 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.306 FMT.9: 3 residues within 4Å: Chain B: P.160, P.196, F.197 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.197

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

EDO.7: 3 residues within 4Å: Chain B: Q.15, W.16, L.18 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.15, B:Q.15 EDO.8: 4 residues within 4Å: Chain B: Q.43, F.71, K.72, Y.75 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schiemann, K., CDK8-CYCC IN COMPLEX WITH [6-Hydroxy-3-(3-methyl-benzyl)-1H-indazol-5-yl]-((S)-3-hydroxy-pyrrolidin-1-yl)-methanone. To Be Published

Release Date

2016-04-27

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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