Research workbench

Dengue serotype 3 RNA-dependent RNA polymerase bound to compound 29

Analyse Dengue serotype 3 RNA-dependent RNA polymerase bound to compound 29 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5I3Q
Type: protein
Length: 585 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Genome polyprotein
UniProt: Q6DLV0
Ligands: 68E, ZN
Pockets: 3 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 51% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Genome polyprotein	protein	585	51% helix, 10% strand	Q6DLV0

Ligands and binding sites

68E · 5-[5-(3-hydroxyprop-1-yn-1-yl)thiophen-2-yl]-4-methoxy-2-methyl-N-[(quinolin-8-yl)sulfonyl]benzamide · ligand · chains A
ZN · Zinc ion · metal · 2 copies · chains A

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

Pockets

3 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	750	0.70	0.76	63	68E
2	214	0.54	0.77	36	empty
3	91	0.47	0.81	22	empty

Compared structures

5I3Q · Dengue serotype 3 RNA-dependent RNA polymerase bound to compound 29 · 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 Q6DLV0
Elsewhere: RCSB PDB 5I3Q · PDBe 5I3Q · UniProt Q6DLV0

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