MolNFT v1 · #68766 · protein

Structure of abl kinase in complex with imatinib and gnf-2

3K5V · Tyrosine-protein kinase ABL1: “Structure of abl kinase in complex with imatinib and gnf-2”. X-ray diffraction, 3 ligands (STJ, STI, CL), 7 pockets (best druggability 0.76). MolNFT v1 #68766 on GenesisL1: 3D structure, binding sites…

PDB: 3K5V
Type: protein
Length: 569 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: P00520
Ligands: STJ, STI, CL
Pockets: 7 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tyrosine-protein kinase ABL1 (EC 2.7.10.2)	protein	286	42% helix, 16% strand	P00520
B	Tyrosine-protein kinase ABL1 (EC 2.7.10.2)	protein	283	42% helix, 16% strand	P00520

Ligands and binding sites

STJ · 3-(6-{[4-(trifluoromethoxy)phenyl]amino}pyrimidin-4-yl)benzamide · ligand · 2 copies · chains A, B
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
CL · Chloride ion · ion · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	728	0.76	0.81	67	STI
2	1171	0.75	0.78	66	empty
3	619	0.74	0.80	55	STI
4	100	0.63	0.88	21	STJ
5	103	0.60	0.86	21	STJ

Interfaces

1 interface between chains.

A–B · 480 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

3K5V · Structure of Abl kinase in complex with imatinib and GNF-2 · the same entry in another collection · chain A against A, TM-score 1.00
P00520 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase ABL1 (P00520) · a predicted model of the same protein · chain B against A, TM-score 0.91

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 P00520
Elsewhere: RCSB PDB 3K5V · PDBe 3K5V · UniProt P00520

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