MolNFT v1 · #114373 · protein

CDK8/CYCC in complex with 8-{3-chloro-5-[4-(1-methyl-1H-pyrazol-4-yl)- phenyl]-pyridin- 4-yl}-2,8-diaza-SPIRO[4.5]DECAN-1-one

5BNJ · Cyclin-dependent kinase 8: “CDK8/CYCC in complex with 8-{3-chloro-5-[4-(1-methyl-1H-pyrazol-4-yl)- phenyl]-pyridin…”. X-ray diffraction, 1 ligand (4TV), 11 pockets (best druggability 0.71). MolNFT v1 #114373 on GenesisL1: 3D…

PDB: 5BNJ
Type: protein
Length: 609 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cyclin-dependent kinase 8; Cyclin-C
EC: 2.7.11.22, 2.7.11.23
UniProt: P49336, P24863
Ligands: 4TV
Pockets: 11 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 51% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cyclin-dependent kinase 8 (EC 2.7.11.22, 2.7.11.23)	protein	343	39% helix, 13% strand	P49336
B	Cyclin-C	protein	266	67% helix, 0% strand	P24863

Ligands and binding sites

4TV · 8-{3-chloro-5-[4-(1-methyl-1H-pyrazol-4-yl)phenyl]pyridin-4-yl}-2,8-diazaspiro[4.5]decan-1-one · ligand · chains A
FMT · Formic acid · additive · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	414	0.71	0.82	40	4TV
2	470	0.69	0.80	56	empty
3	163	0.48	0.76	22	empty
4	97	0.41	0.77	14	FMT
5	80	0.40	0.79	15	empty

Interfaces

1 interface between chains.

A–B · 1746 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

5BNJ · CDK8/CYCC IN COMPLEX WITH 8-{3-Chloro-5-[4-(1-methyl-1H-pyrazol-4-yl)-phenyl]-pyridin… · the same entry in another collection · chain A against A, TM-score 1.00
P24863 · AlphaFold monomer V2.0 prediction for cyclin-C (P24863) · a predicted model of the same protein · chain B against A, TM-score 0.99
P49336 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase 8 (P49336) · a predicted model of the same protein · chain A against A, TM-score 0.97

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P49336
Every structure of UniProt P24863
Elsewhere: RCSB PDB 5BNJ · PDBe 5BNJ · UniProt P49336 · UniProt P24863

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