MolNFT v1 · #77254 · protein

CDK2 in complex with inhibitor rc-2-135

3R9D · Cyclin-dependent kinase 2: “CDK2 in complex with inhibitor rc-2-135”. X-ray diffraction, 1 ligand (X6B), 3 pockets (best druggability 0.73). MolNFT v1 #77254 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3R9D
Type: protein
Length: 294 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: X6B
Pockets: 3 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cyclin-dependent kinase 2 (EC 2.7.11.22)	protein	294	33% helix, 16% strand	P24941

Ligands and binding sites

X6B · 4-amino-N-(3-fluorophenyl)-2-[(4-sulfamoylphenyl)amino]-1,3-thiazole-5-carboxamide · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	320	0.73	0.85	45	X6B
2	163	0.58	0.82	25	empty
3	95	0.43	0.78	22	empty

Compared structures

3R9D · CDK2 in complex with inhibitor RC-2-135 · 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 3R9D · PDBe 3R9D · UniProt P24941

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