MolNFT v1 · #110951 · protein

CDK1/CKS1

4YC6 · Cyclin-dependent kinase 1: “CDK1/CKS1”. X-ray diffraction, 17 pockets (best druggability 0.81). MolNFT v1 #110951 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4YC6
Type: protein
Length: 1,420 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cyclin-dependent kinase 1; Cyclin-dependent kinases regulatory subunit 1
EC: 2.7.11.22, 2.7.11.23
UniProt: P06493, P61024
Pockets: 17 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G	Cyclin-dependent kinase 1 (EC 2.7.11.22, 2.7.11.23)	protein	285	35% helix, 16% strand	P06493
B, D, F, H	Cyclin-dependent kinases regulatory subunit 1	protein	70	16% helix, 31% strand	P61024

Pockets

17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	677	0.81	0.85	71	empty
2	675	0.81	0.85	69	empty
3	831	0.80	0.83	71	empty
4	1075	0.79	0.80	70	empty
5	744	0.75	0.80	85	empty

Interfaces

16 interfaces between chains.

A–G · 1265 Å² buried · 25 hydrogen bonds · protein-protein
C–E · 1195 Å² buried · 22 hydrogen bonds · protein-protein
G–H · 787 Å² buried · 14 hydrogen bonds · protein-protein
E–F · 786 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 782 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

4YC6 · CDK1/CKS1 · the same entry in another collection · chain H against H, TM-score 1.00
P06493 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase 1 (P06493) · a predicted model of the same protein · chain E against A, TM-score 0.96

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 P61024
Elsewhere: RCSB PDB 4YC6 · PDBe 4YC6 · UniProt P06493 · UniProt P61024

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