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Structure determination of antiviral compound sch 38057 complexed with human rhinovirus 14

Analyse Structure determination of antiviral compound sch 38057 complexed with human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1HRI
Type: protein
Length: 804 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Human rhinovirus 14 coat protein (subunit VP1); Human rhinovirus 14 coat protein (subunit…
UniProt: P03303
Ligands: S57
Pockets: 10 · best druggability 0.81

Structure

x-ray diffraction · 4 distinct chains · 11% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	Human rhinovirus 14 coat protein (subunit VP1)	protein	273	9% helix, 31% strand	P03303
2	Human rhinovirus 14 coat protein (subunit VP2)	protein	255	15% helix, 37% strand	P03303
3	Human rhinovirus 14 coat protein (subunit VP3)	protein	236	9% helix, 32% strand	P03303
4	Human rhinovirus 14 coat protein (subunit VP4)	protein	40	18% helix, 3% strand	P03303

Ligands and binding sites

S57 · 1-[6-(2-chloro-4-methyxyphenoxy)-hexyl]-imidazole · ligand · chains 1, 3

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

Pockets

10 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	531	0.81	0.87	82	S57
2	159	0.46	0.76	33	empty
3	142	0.43	0.75	31	empty
4	84	0.41	0.79	16	empty
5	118	0.41	0.76	21	empty

Interfaces

6 interfaces between chains.

1–3 · 4154 Å² buried · 75 hydrogen bonds · protein-protein
1–2 · 2107 Å² buried · 45 hydrogen bonds · protein-protein
2–3 · 1705 Å² buried · 15 hydrogen bonds · protein-protein
1–4 · 968 Å² buried · 14 hydrogen bonds · protein-protein
3–4 · 913 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

1HRI · Structure determination of antiviral compound sch 38057 complexed with human rhinovirus 14 · the same entry in another collection · chain 3 against 3, 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 1HRI · PDBe 1HRI · UniProt P03303

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