MolNFT v1 · #20924 · protein

Rhinovirus 14 mutant N1105S complexed with antiviral compound win 52084

1RUD: “Rhinovirus 14 mutant N1105S complexed with antiviral compound win 52084”. X-ray diffraction, 1 ligand (W84), 9 pockets (best druggability 0.79). MolNFT v1 #20924 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1RUD
Type: protein
Length: 804 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rhinovirus 14
UniProt: P03303
Ligands: W84
Pockets: 9 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 12% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	Rhinovirus 14	protein	273	10% helix, 32% strand	P03303
2	Rhinovirus 14	protein	255	15% helix, 37% strand	P03303
3	Rhinovirus 14	protein	236	9% helix, 32% strand	P03303
4	Rhinovirus 14	protein	40	18% helix, 3% strand	P03303

Ligands and binding sites

W84 · 5-(7-(5-hydro-4-methyl-2-oxazolyl)phenoxy)heptyl)-3-methyl isoxazole · ligand · chains 1, 3

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

Pockets

9 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	449	0.79	0.87	69	W84
2	168	0.47	0.76	34	empty
3	90	0.42	0.78	18	empty
4	110	0.40	0.76	21	empty
5	115	0.39	0.75	25	empty

Interfaces

6 interfaces between chains.

1–3 · 4142 Å² buried · 70 hydrogen bonds · protein-protein
1–2 · 2108 Å² buried · 44 hydrogen bonds · protein-protein
2–3 · 1705 Å² buried · 15 hydrogen bonds · protein-protein
1–4 · 954 Å² buried · 14 hydrogen bonds · protein-protein
3–4 · 898 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

1RUD · Rhinovirus 14 mutant N1105S complexed with antiviral compound win 52084 · the same entry in another collection · chain 1 against 1, 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 P03303
Elsewhere: RCSB PDB 1RUD · PDBe 1RUD · UniProt P03303

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