Research workbench

Dengue-RDRP3-inhibitor complex soaking

Analyse Dengue-RDRP3-inhibitor complex soaking in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6H9R
Type: protein
Length: 558 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Genome polyprotein
EC: 3.4.21.91, 3.6.1.15, 3.6.4.13, 2.1.1.56, 2.1.1.57, 2.7.7.48
UniProt: Q6YMS4
Ligands: 5V5, ZN
Pockets: 5 · best druggability 0.68

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Genome polyprotein (EC 3.4.21.91, 3.6.1.15, 3.6.4.13, 2.1.1.56, 2.1.1.57, 2.7.7.48)	protein	558	49% helix, 9% strand	Q6YMS4

Ligands and binding sites

5V5 · 2-(4-methoxy-3-thiophen-2-yl-phenyl)ethanoic acid · ligand · chains A
ZN · Zinc ion · metal · 2 copies · chains A
PEG · Di(hydroxyethyl)ether · additive · 8 copies · chains A

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

Pockets

5 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	653	0.68	0.76	68	5V5
2	146	0.58	0.83	32	empty
3	59	0.48	0.85	15	empty
4	56	0.29	0.75	15	empty
5	54	0.29	0.75	18	empty

Compared structures

6H9R · Dengue-RdRp3-inhibitor complex soaking · 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 Q6YMS4
Elsewhere: RCSB PDB 6H9R · PDBe 6H9R · UniProt Q6YMS4

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