MolNFT v1 · #37469 · protein

A src-like inactive conformation in the abl tyrosine kinase domain

2G2F · Abl kinase: “A src-like inactive conformation in the abl tyrosine kinase domain”. X-ray diffraction, 2 ligands (AGS, 112), 5 pockets (best druggability 0.76). MolNFT v1 #37469 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 2G2F
Type: protein
Length: 547 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Abl kinase; ATP-peptide conjugate
UniProt: P00519
Ligands: AGS, 112
Pockets: 5 · best druggability 0.76

Structure

x-ray diffraction · 3 distinct chains · 41% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Abl kinase	protein	275	44% helix, 20% strand	P00519
B	Abl kinase	protein	264	39% helix, 20% strand	P00519
C	ATP-peptide conjugate	protein	8	0% helix, 25% strand	—

Ligands and binding sites

AGS · Phosphothiophosphoric acid-adenylate ester · ligand · chains B
112 · Thiophosphoric acid O-((adenosyl-phospho)phospho)-S-acetamidyl-diester · ligand · chains A, C

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	772	0.76	0.80	59	112
2	253	0.63	0.81	22	AGS
3	82	0.48	0.82	20	empty
4	79	0.48	0.82	18	empty
5	176	0.47	0.75	24	empty

Interfaces

1 interface between chains.

A–C · 478 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

2G2F · A Src-like Inactive Conformation in the Abl Tyrosine Kinase Domain · 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 0.97

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 2G2F · PDBe 2G2F · UniProt P00519

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