MolNFT v1 · #104993 · protein

Structure of methionyl-tRNA synthetase in complex with 1-(4-{4-[(1H- benzimidazol-2-YLMETHYL)AMINO]-6-(4,5-dimethoxy-2-methylphenoxy) pyrimidin-2-YL}PIPERAZIN-1-YL)ETHANONE

4QRE: “Structure of methionyl-tRNA synthetase in complex with 1-(4-{4-[(1H…”. X-ray diffraction, 3 ligands (3BG, ATP, MG), 2 pockets (best druggability 0.77). MolNFT v1 #104993 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4QRE
Type: protein
Length: 519 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Methionyl-tRNA synthetase
EC: 6.1.1.10
UniProt: W8U1H8
Ligands: 3BG, ATP, MG
Pockets: 2 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 51% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Methionyl-tRNA synthetase (EC 6.1.1.10)	protein	519	51% helix, 17% strand	W8U1H8

Ligands and binding sites

3BG · 1-(4-{4-[(1H-benzimidazol-2-ylmethyl)amino]-6-(4,5-dimethoxy-2-methylphenoxy)pyrimidin-2-yl}piperazin-1-yl)ethanone · ligand · chains A
ATP · Adenosine-5'-triphosphate · ligand · chains A
MG · Magnesium ion · metal · 2 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1110	0.77	0.79	79	3BG, ATP, MG
2	60	0.33	0.76	13	empty

Compared structures

4QRE · Structure of Methionyl-tRNA Synthetase in complex with… · 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 W8U1H8
Elsewhere: RCSB PDB 4QRE · PDBe 4QRE · UniProt W8U1H8

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