SMTL ID : 9h8c.1

Human CDK8/Cyclin-C complex with inhibitor 2-9

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.57 Å

Oligo State

hetero-1-1-mer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: Y.144, F.346, P.352 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: K.85, H.86, P.87, S.91, E.176, R.179 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.86, A:S.91, A:S.91, A:E.176, A:R.179 GOL.6: 7 residues within 4Å: Chain B: A.30, M.31, A.32, Q.90, Y.183, H.184, R.187 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.30, B:H.184, B:R.187 Water bridges: B:R.187

1 x 01: 4-[(3~{S})-3-[2-[(3~{R})-3-fluoranylpyrrolidin-1-yl]pyrimidin-4-yl]piperidin-1-yl]carbonyl-1~{H}-pyrrole-2-carbonitrile

01.3: 13 residues within 4Å: Chain A: V.38, Y.43, V.46, A.61, K.63, F.108, D.114, A.166, N.167, L.169, A.183, D.184, R.367 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.38, A:F.108 Hydrogen bonds: A:K.63 Water bridges: A:N.167 pi-Stacking: A:Y.43

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

DMS.4: 3 residues within 4Å: Chain B: L.203, P.204, W.207 1 PLIP interactions: 1 interactions with chain B pi-Cation interactions: B:W.207 DMS.5: 7 residues within 4Å: Chain B: H.233, C.236, V.237, K.241, D.242, A.243, R.244 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nicolle, S. et al., Phenotype-Led Identification of IL-10 Upregulators in Human CD4 + T-cells and Elucidation of Their Pharmacology as Highly Selective CDK8/CDK19 Inhibitors. J.Med.Chem. (2025)

Release Date

2025-01-22

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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