Research workbench

Abl kinase in complex with imatinib and fragment (FRAG2) in the myristate site

Analyse Abl kinase in complex with imatinib and fragment (FRAG2) in the myristate site in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3MSS
Type: protein
Length: 1,056 residues
Chains: 4
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: STI, MS7
Pockets: 14 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Tyrosine-protein kinase ABL1 (EC 2.7.10.2)	protein	264	44% helix, 17% strand	P00520

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 · 4 copies · chains A, B, C, D
MS7 · O-benzyl-N-methyl-L-tyrosinamide · ligand · 4 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	553	0.74	0.81	57	STI
2	548	0.73	0.81	60	STI
3	538	0.73	0.81	64	STI
4	551	0.73	0.80	56	STI
5	554	0.64	0.75	39	empty

Interfaces

4 interfaces between chains.

A–C · 294 Å² buried · 1 hydrogen bond · protein-protein
C–D · 176 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 123 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 87 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

3MSS · Abl kinase in complex with imatinib and fragment (FRAG2) in the myristate site · the same entry in another collection · chain D against D, TM-score 1.00
P00520 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase ABL1 (P00520) · a predicted model of the same protein · chain D 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 3MSS · PDBe 3MSS · UniProt P00520

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