MolNFT v1 · #129565 · protein

CDK2(F80C, C177A) with covalent ligand at F80C

5OO3 · Cyclin-dependent kinase 2: “CDK2(F80C, C177A) with covalent ligand at F80C”. X-ray diffraction, 1 ligand (9ZB), 3 pockets (best druggability 0.77). MolNFT v1 #129565 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5OO3
Type: protein
Length: 286 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cyclin-dependent kinase 2
EC: 2.7.11.22
UniProt: P24941
Ligands: 9ZB
Pockets: 3 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cyclin-dependent kinase 2 (EC 2.7.11.22)	protein	286	36% helix, 17% strand	P24941

Ligands and binding sites

9ZB · 1-(4-ethyl-2,3-dihydroquinoxalin-1-yl)propan-1-one · ligand · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	271	0.77	0.89	40	9ZB
2	80	0.38	0.77	17	empty
3	64	0.33	0.76	16	empty

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

5OO3 · Cdk2(F80C, C177A) with covalent ligand at F80C · the same entry in another collection · chain A against A, TM-score 1.00
P24941 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase 2 (P24941) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 P24941
Elsewhere: RCSB PDB 5OO3 · PDBe 5OO3 · UniProt P24941

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