SMTL ID : 9h8s.1

Human CDK8/Cyclin-C complex with inhibitor 3-7

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.16 Å

Oligo State

hetero-1-1-mer

Ligands

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 1 residues within 4Å: Chain A: M.329 Ligand excluded by PLIP

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

EDO.2: 3 residues within 4Å: Chain A: K.85, H.86, P.87 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.86, A:S.91 Water bridges: A:H.86 EDO.3: 4 residues within 4Å: Chain A: H.99, R.102 Chain B: E.167, Y.171 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.99, A:R.102 EDO.4: 4 residues within 4Å: Chain A: M.291, K.292, F.294, R.295 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.295 Water bridges: A:K.292, A:D.293 EDO.5: 7 residues within 4Å: Chain A: Y.43, K.63, I.65, S.73, E.77, D.184, G.186 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.43, A:D.184, A:G.186 EDO.6: 4 residues within 4Å: Chain A: Y.144, F.346, L.347, P.352 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.144 EDO.7: 5 residues within 4Å: Chain A: R.82, E.83, K.85 Chain B: Q.37, S.39 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.82 EDO.12: 7 residues within 4Å: Chain B: A.30, A.32, Q.90, I.181, V.182, Y.183, R.187 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.90, B:R.187 Water bridges: B:E.128

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 2 residues within 4Å: Chain A: W.116 Ligands: 01.9 No protein-ligand interaction detected (PLIP)

1 x 01: 4-[(3~{S},5~{R})-3-[2-[(3~{R})-3-fluoranylpyrrolidin-1-yl]pyrimidin-4-yl]-5-methoxy-piperidin-1-yl]carbonyl-1~{H}-pyrrole-2-carbonitrile

01.9: 15 residues within 4Å: Chain A: V.38, Y.43, V.46, A.61, K.63, I.90, F.108, A.111, D.114, H.117, A.166, L.169, D.184, R.367 Ligands: GOL.8 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.90, 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.10: 3 residues within 4Å: Chain B: L.203, P.204, W.207 2 PLIP interactions: 2 interactions with chain B pi-Cation interactions: B:W.207, B:W.207 DMS.11: 6 residues within 4Å: Chain B: H.233, C.236, V.237, K.241, 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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