Research workbench

CDK2 in complex with FRAGLITE35

Analyse CDK2 in complex with FRAGLITE35 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6Q4I
Type: protein
Length: 288 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: HGK
Pockets: 3 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cyclin-dependent kinase 2 (EC 2.7.11.22)	protein	288	37% helix, 16% strand	P24941

Ligands and binding sites

HGK · 2-[4-[(2-oxidanylidene-3~{H}-pyridin-4-yl) oxy]phenyl]ethanoic acid · ligand · chains A
DMS · Dimethyl sulfoxide · additive · 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	368	0.69	0.82	49	HGK
2	68	0.39	0.79	18	empty
3	66	0.34	0.76	13	empty

Compared structures

6Q4I · CDK2 in complex with FragLite35 · 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 6Q4I · PDBe 6Q4I · UniProt P24941

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