MolNFT v1 · #121158 · protein

Dengue serotype 3 RNA-dependent RNA polymerase bound to compound 23

5HMZ · RNA-directed RNA polymerase NS5: “Dengue serotype 3 RNA-dependent RNA polymerase bound to compound 23”. X-ray diffraction, 2 ligands (LNZ, ZN), 4 pockets (best druggability 0.69). MolNFT v1 #121158 on GenesisL1: 3D structure…

PDB: 5HMZ
Type: protein
Length: 585 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA-directed RNA polymerase NS5
EC: 2.7.7.48
UniProt: Q6DLV0
Ligands: LNZ, ZN
Pockets: 4 · best druggability 0.69

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA-directed RNA polymerase NS5 (EC 2.7.7.48)	protein	585	51% helix, 10% strand	Q6DLV0

Ligands and binding sites

LNZ · 5-(5-(3-hydroxyprop-1-yn-1-yl)thiophen-2-yl)-4-methoxy-2-methyl-N-(methylsulfonyl)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

4 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	761	0.69	0.76	70	LNZ
2	175	0.49	0.76	23	empty
3	103	0.48	0.80	22	empty
4	61	0.42	0.81	17	empty

Compared structures

5HMZ · Dengue serotype 3 RNA-dependent RNA polymerase bound to compound 23 · 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 5HMZ · PDBe 5HMZ · UniProt Q6DLV0

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