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A comparison of the anti-rhinoviral drug binding pocket in HRV14 and HRV1A

Analyse A comparison of the anti-rhinoviral drug binding pocket in HRV14 and HRV1A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2HWC
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: W54
Pockets: 11 · best druggability 0.78

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	10% helix, 33% 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

W54 · 5-(5-(2,6-dichloro-4-(4,5-dihydro-2-oxazoly)phenoxy)pentyl)-3-methyl isoxazole · ligand · chains 1, 3

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

Pockets

11 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	342	0.78	0.88	45	W54
2	190	0.52	0.78	32	empty
3	174	0.47	0.76	35	empty
4	143	0.43	0.75	30	empty
5	118	0.41	0.76	21	empty

Interfaces

6 interfaces between chains.

1–3 · 4121 Å² buried · 69 hydrogen bonds · protein-protein
1–2 · 2103 Å² buried · 42 hydrogen bonds · protein-protein
2–3 · 1695 Å² buried · 14 hydrogen bonds · protein-protein
1–4 · 953 Å² buried · 14 hydrogen bonds · protein-protein
3–4 · 898 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

2HWC · A comparison of the anti-rhinoviral drug binding pocket in HRV14 and HRV1A · 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 2HWC · PDBe 2HWC · UniProt P03303

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