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Plasmodium vivax N-myristoyltransferase in complex with a benzothiophene inhibitor (compound 20B)

Analyse Plasmodium vivax N-myristoyltransferase in complex with a benzothiophene… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4CAE
Type: protein
Length: 1,135 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycylpeptide N-tetradecanoyltransferase
EC: 2.3.1.97
UniProt: A5K1A2
Ligands: 3F3, NHW, MG, CL, SO4
Pockets: 9 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 27% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97)	protein	384	27% helix, 30% strand	A5K1A2
C	Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97)	protein	367	27% helix, 31% strand	A5K1A2

Ligands and binding sites

3F3 · 4-[(2-{5-[(3-methoxyphenyl)methyl]-1,3,4-oxadiazol-2-yl}-1-benzothiophen-3-yl)oxy]piperidine · ligand · 3 copies · chains A, B, C
NHW · 2-oxopentadecyl-CoA · ligand · 3 copies · chains A, B, C
MG · Magnesium ion · metal · 3 copies · chains A, B, C
CL · Chloride ion · ion · 4 copies · chains A, B, C
SO4 · Sulfate ion · ion · chains A, B
DMS · Dimethyl sulfoxide · additive · 3 copies · chains A, B, C

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

Pockets

9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	950	0.80	0.82	90	empty
2	872	0.80	0.82	87	MG, 3F3, NHW
3	899	0.79	0.81	86	MG, 3F3, NHW
4	805	0.79	0.82	71	MG, 3F3, NHW
5	124	0.40	0.74	18	empty

Interfaces

2 interfaces between chains.

A–B · 483 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 120 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4CAE · Plasmodium vivax N-myristoyltransferase in complex with a benzothiophene 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 A5K1A2
Elsewhere: RCSB PDB 4CAE · PDBe 4CAE · UniProt A5K1A2

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