MolNFT v1 · #150454 · protein

CDK1/CYCLINB/CKS2 in complex with CGP74514A

6GU4 · Cyclin-dependent kinase 1: “CDK1/CYCLINB/CKS2 in complex with CGP74514A”. X-ray diffraction, 1 ligand (FC8), 9 pockets (best druggability 0.81). MolNFT v1 #150454 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6GU4
Type: protein
Length: 630 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cyclin-dependent kinase 1; G2/MITOTIC-specific cyclin-B1; Cyclin-dependent kinases…
EC: 2.7.11.22, 2.7.11.23
UniProt: P06493, P14635, P33552
Ligands: FC8
Pockets: 9 · best druggability 0.81

Structure

x-ray diffraction · 3 distinct chains · 46% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cyclin-dependent kinase 1 (EC 2.7.11.22, 2.7.11.23)	protein	292	33% helix, 17% strand	P06493
B	G2/MITOTIC-specific cyclin-B1	protein	264	68% helix, 0% strand	P14635
C	Cyclin-dependent kinases regulatory subunit 2	protein	74	15% helix, 36% strand	P33552

Ligands and binding sites

FC8 · ~{N}2-[(1~{R},2~{S})-2-azanylcyclohexyl]-~{N}6-(3-chlorophenyl)-9-ethyl-purine-2,6-diamine · ligand · chains A

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

Pockets

9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	176	0.81	0.96	26	empty
2	267	0.70	0.84	31	FC8
3	285	0.54	0.75	39	empty
4	104	0.46	0.79	17	empty
5	170	0.45	0.75	24	empty

Interfaces

2 interfaces between chains.

A–B · 1512 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 753 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

6GU4 · CDK1/CyclinB/Cks2 in complex with CGP74514A · the same entry in another collection · chain A against A, TM-score 1.00
P14635 · AlphaFold monomer V2.0 prediction for G2/MITOTIC-specific cyclin-B1 (P14635) · a predicted model of the same protein · chain B against A, TM-score 0.99
P33552 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinases regulatory subunit 2… · a predicted model of the same protein · chain C against A, TM-score 0.93
P06493 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase 1 (P06493) · a predicted model of the same protein · chain A against A, TM-score 0.93

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 P06493
Every structure of UniProt P14635
Every structure of UniProt P33552
Elsewhere: RCSB PDB 6GU4 · PDBe 6GU4 · UniProt P06493 · UniProt P14635 · UniProt P33552

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.