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C-helix-out binding of dasatinib analog to C-abl kinase

Analyse C-helix-out binding of dasatinib analog to C-abl kinase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4YC8
Type: protein
Length: 523 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tyrosine-protein kinase ABL1
EC: 2.7.10.2
UniProt: P00519
Ligands: 4B7
Pockets: 5 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tyrosine-protein kinase ABL1 (EC 2.7.10.2)	protein	259	42% helix, 18% strand	P00519
B	Tyrosine-protein kinase ABL1 (EC 2.7.10.2)	protein	264	39% helix, 18% strand	P00519

Ligands and binding sites

4B7 · 2-({6-[4-(2-hydroxyethyl)piperazin-1-yl]-2-methylpyrimidin-4-yl}amino)-N-(4-phenoxyphenyl)-1,3-thiazole-5-carboxamide · ligand · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, 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	1067	0.70	0.75	77	empty
2	273	0.54	0.76	32	4B7, EDO
3	54	0.50	0.86	15	empty
4	174	0.50	0.77	29	4B7
5	50	0.44	0.84	16	empty

Interfaces

1 interface between chains.

A–B · 372 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4YC8 · C-Helix-Out Binding of Dasatinib Analog to c-Abl Kinase · the same entry in another collection · chain A against A, TM-score 1.00
P00519 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase ABL1 (P00519) · a predicted model of the same protein · chain B against A, TM-score 0.96

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 P00519
Elsewhere: RCSB PDB 4YC8 · PDBe 4YC8 · UniProt P00519

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