MolNFT v1 · #189386 · protein

The structure of cyclin-dependent kinase 5 (CDK5) in complex with P25 and compound 7

7VDQ: “The structure of cyclin-dependent kinase 5 (CDK5) in complex with P25 and compound 7”. X-ray diffraction, 1 ligand (64V). MolNFT v1 #189386 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7VDQ
Type: protein
Length: 851 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
UniProt: Q00535, Q15078
Ligands: 64V

Structure

x-ray diffraction · 4 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	—	protein	290	—	Q00535
B	—	protein	277	—	Q00535
C	—	protein	148	—	Q15078
D	—	protein	136	—	Q15078

Ligands and binding sites

64V · 2-[[7-[[2-fluoranyl-4-[3-(hydroxymethyl)pyrazol-1-yl]phenyl]amino]-1,6-naphthyridin-2-yl]-(1-methylpiperidin-4-yl)amino]ethanoic acid · ligand · 2 copies · chains A, B

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

Compared structures

7VDQ · The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 7 · the same entry in another collection · chain D against D, TM-score 1.00
Q15078 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase 5 activator 1 (Q15078) · a predicted model of the same protein · chain C against A, TM-score 1.00
Q00535 · AlphaFold monomer V2.0 prediction for cyclin-dependent-like kinase 5 (Q00535) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q00535
Every structure of UniProt Q15078
Elsewhere: RCSB PDB 7VDQ · PDBe 7VDQ · UniProt Q00535 · UniProt Q15078

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