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C-abl kinase domain with the ACTIVATOR(CMPD6), 2-cyano-N-(4-(3,4- DICHLOROPHENYL)THIAZOL-2-YL)ACETAMIDE

Analyse C-abl kinase domain with the ACTIVATOR(CMPD6), 2-cyano-N-(4-(3,4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6NPE
Type: protein
Length: 520 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: STI, KWD, SO4
Pockets: 5 · best druggability 0.76

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tyrosine-protein kinase ABL1 (EC 2.7.10.2)	protein	264	44% helix, 17% strand	P00519
B	Tyrosine-protein kinase ABL1 (EC 2.7.10.2)	protein	256	48% helix, 15% strand	P00519

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
KWD · 2-cyano-~{N}-[4-(3,4-dichlorophenyl)-1,3-thiazol-2-yl]ethanamide · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 4 copies · chains A, B
2PE · Nonaethylene glycol · 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	764	0.76	0.80	86	STI
2	300	0.73	0.85	31	STI
3	258	0.61	0.80	33	KWD
4	86	0.50	0.82	19	KWD
5	100	0.41	0.77	21	empty

Interfaces

1 interface between chains.

A–B · 1105 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

6NPE · C-abl Kinase domain with the activator(cmpd6)… · 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 0.92

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 6NPE · PDBe 6NPE · UniProt P00519

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