MolNFT v1 · #75724 · protein

Discovery and characterization of a cell-permeable, small-molecule C- abl kinase activator that binds to the myristoyl binding site

3PYY · V-abl abelson murine leukemia viral oncogene homolog 1…: “Discovery and characterization of a cell-permeable, small-molecule C- abl kinase activator that binds to the…”. X-ray diffraction, 3 ligands (STI, 3YY, SO4), 5 pockets (best…

PDB: 3PYY
Type: protein
Length: 522 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: V-abl abelson murine leukemia viral oncogene homolog 1 isoform B variant
UniProt: Q59FK4
Ligands: STI, 3YY, SO4
Pockets: 5 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 46% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	V-abl abelson murine leukemia viral oncogene homolog 1 isoform B variant	protein	265	45% helix, 17% strand	Q59FK4
B	V-abl abelson murine leukemia viral oncogene homolog 1 isoform B variant	protein	257	48% helix, 15% strand	Q59FK4

Ligands and binding sites

STI · 4-(4-methyl-piperazin-1-ylmethyl)-N-[4-methyl-3-(4-pyridin-3-yl-pyrimidin-2-ylamino)-phenyl]-benzamide · ligand · 2 copies · chains A, B
3YY · (5R)-5-[3-(4-fluorophenyl)-1-phenyl-1H-pyrazol-4-yl]imidazolidine-2,4-dione · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 3 copies · chains A, B
2PE · Nonaethylene glycol · additive · chains B
GOL · Glycerol · additive · chains B

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	791	0.78	0.81	95	STI, 3YY
2	316	0.72	0.84	35	STI
3	87	0.53	0.83	16	3YY
4	110	0.42	0.77	17	empty
5	88	0.41	0.78	21	empty

Interfaces

1 interface between chains.

A–B · 1050 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

3PYY · Discovery and Characterization of a Cell-Permeable, Small-molecule c-Abl Kinase Activator… · the same entry in another collection · chain A against A, TM-score 1.00

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 Q59FK4
Elsewhere: RCSB PDB 3PYY · PDBe 3PYY · UniProt Q59FK4

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