MolNFT v1 · #169473 · protein

Dengue serotype 3 RNA-dependent RNA polymerase bound to nitd-640

6XD1: “Dengue serotype 3 RNA-dependent RNA polymerase bound to nitd-640”. X-ray diffraction, 2 ligands (V0J, ZN), 3 pockets (best druggability 0.78). MolNFT v1 #169473 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6XD1
Type: protein
Length: 599 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA-dependent RNA polymerase
UniProt: A1XTB9
Ligands: V0J, ZN
Pockets: 3 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA-dependent RNA polymerase	protein	599	49% helix, 10% strand	A1XTB9

Ligands and binding sites

V0J · (2R)-4-(butyl{[2'-(1H-tetrazol-5-yl)[1,1'-biphenyl]-4-yl]methyl}carbamoyl)-1-(2,2-diphenylpropanoyl) piperazine-2-carboxylic acid · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1187	0.78	0.79	110	V0J
2	119	0.46	0.78	23	empty
3	72	0.45	0.81	18	empty

Compared structures

6XD1 · Dengue serotype 3 RNA-dependent RNA polymerase bound to NITD-640 · 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 A1XTB9
Elsewhere: RCSB PDB 6XD1 · PDBe 6XD1 · UniProt A1XTB9

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