MolNFT v1 · #161090 · protein

CDK2 in complex with FRAGLITE1

6Q3C · Cyclin-dependent kinase 2: “CDK2 in complex with FRAGLITE1”. X-ray diffraction, 1 ligand (BYZ), 3 pockets (best druggability 0.67). MolNFT v1 #161090 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6Q3C
Type: protein
Length: 289 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: BYZ
Pockets: 3 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cyclin-dependent kinase 2 (EC 2.7.11.22)	protein	289	36% helix, 14% strand	P24941

Ligands and binding sites

BYZ · 4-bromo-1H-pyrazole · ligand · 2 copies · 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	318	0.67	0.81	37	BYZ
2	57	0.37	0.79	17	empty
3	55	0.37	0.79	14	empty

Modifications

Observed in the structure: 1 modified (oxidation).

Compared structures

6Q3C · CDK2 in complex with FragLite1 · 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 6Q3C · PDBe 6Q3C · UniProt P24941

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