MolNFT v1 · #161398 · protein

Leishmania major N-myristoyltransferase in complex with thienopyrimidine inhibitor imp-0000081

6QDB · Glycylpeptide N-tetradecanoyltransferase: “Leishmania major N-myristoyltransferase in complex with thienopyrimidine inhibitor imp-0000081”. X-ray diffraction, 3 ligands (HWQ, MYA, MG), 2 pockets (best druggability 0.79). MolNFT v1…

PDB: 6QDB
Type: protein
Length: 411 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycylpeptide N-tetradecanoyltransferase
EC: 2.3.1.97
UniProt: Q4Q5S8
Ligands: HWQ, MYA, MG
Pockets: 2 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97)	protein	411	32% helix, 28% strand	Q4Q5S8

Ligands and binding sites

HWQ · 3-[methyl-[2-[methyl(piperidin-4-yl)amino]thieno[3,2-d]pyrimidin-4-yl]amino]propanenitrile · ligand · 2 copies · chains A
MYA · Tetradecanoyl-coa · ligand · chains A
MG · Magnesium ion · metal · 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	1038	0.79	0.80	92	MYA, HWQ, MG
2	136	0.44	0.76	23	empty

Compared structures

6QDB · Leishmania major N-myristoyltransferase in complex with thienopyrimidine inhibitor… · 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 Q4Q5S8
Elsewhere: RCSB PDB 6QDB · PDBe 6QDB · UniProt Q4Q5S8

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