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Structure of C-met with pyrimidone inhibitor 7

Analyse Structure of C-met with pyrimidone inhibitor 7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3EFJ
Type: protein
Length: 551 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hepatocyte growth factor receptor
EC: 2.7.10.1
UniProt: P08581
Ligands: MT3
Pockets: 2 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hepatocyte growth factor receptor (EC 2.7.10.1)	protein	276	39% helix, 15% strand	P08581
B	Hepatocyte growth factor receptor (EC 2.7.10.1)	protein	275	40% helix, 16% strand	P08581

Ligands and binding sites

MT3 · 2-benzyl-5-{4-[(6,7-dimethoxyquinolin-4-yl)oxy]-3-fluorophenyl}-3-methylpyrimidin-4(3H)-one · ligand · 2 copies · chains A, B

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

Pockets

2 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	499	0.75	0.83	48	MT3
2	614	0.72	0.79	55	MT3

Interfaces

1 interface between chains.

A–B · 938 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

3EFJ · Structure of c-Met with pyrimidone inhibitor 7 · the same entry in another collection · chain A against A, TM-score 1.00

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 P08581
Elsewhere: RCSB PDB 3EFJ · PDBe 3EFJ · UniProt P08581

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