MolNFT v1 · #18131 · protein

Crystal structure of human cyclin-dependent kinase 2 complexed with a nucleoside inhibitor

1PF8 · Cell division protein kinase 2: “Crystal structure of human cyclin-dependent kinase 2 complexed with a nucleoside inhibitor”. X-ray diffraction, 1 ligand (SU9), 2 pockets (best druggability 0.72). MolNFT v1 #18131 on GenesisL1: 3D…

PDB: 1PF8
Type: protein
Length: 298 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cell division protein kinase 2
EC: 2.7.1.37
UniProt: P24941
Ligands: SU9
Pockets: 2 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cell division protein kinase 2 (EC 2.7.1.37)	protein	298	32% helix, 15% strand	P24941

Ligands and binding sites

SU9 · (3Z)-3-(1H-imidazol-5-ylmethylene)-5-methoxy-1H-indol-2(3H)-one · ligand · chains A

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

Pockets

2 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	442	0.72	0.82	48	SU9
2	65	0.36	0.77	15	empty

Compared structures

1PF8 · Crystal Structure of Human Cyclin-Dependent Kinase 2 Complexed with a Nucleoside Inhibitor · 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 0.93

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 P24941
Elsewhere: RCSB PDB 1PF8 · PDBe 1PF8 · UniProt P24941

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