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Denguev-2 capsid ST148 inhibitor complex

Analyse Denguev-2 capsid ST148 inhibitor complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6VG5
Type: protein
Length: 162 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Capsid premembrane protein
UniProt: A0A2D2BF61
Ligands: QWY, NO3
Pockets: 3 · best druggability 0.66

Structure

x-ray diffraction · 1 distinct chain · 70% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Capsid premembrane protein	protein	81	70% helix, 0% strand	A0A2D2BF61

Ligands and binding sites

QWY · 3-amino-N-(5-phenyl-1,3,4-thiadiazol-2-yl)-6,7,8,9-tetrahydro-5H-cyclohepta[b]thieno[3,2-e]pyridine-2-carboxamide · ligand · chains A, B
NO3 · Nitrate ion · ion · 14 copies · chains A, B
GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

3 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	177	0.66	0.85	18	QWY
2	70	0.37	0.78	13	NO3, GOL
3	51	0.31	0.76	11	NO3

Interfaces

1 interface between chains.

A–B · 2530 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

6VG5 · DengueV-2 Capsid ST148 inhibitor Complex · 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 A0A2D2BF61
Elsewhere: RCSB PDB 6VG5 · PDBe 6VG5 · UniProt A0A2D2BF61

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