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Refined crystal structure of human rhinovirus 16 complexed with VP63843 (pleconaril), an anti-picornaviral drug currently in clinical trials

Analyse Refined crystal structure of human rhinovirus 16 complexed with VP63843… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1C8M
Type: protein
Length: 804 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Human rhinovirus 16 coat protein
UniProt: Q82122
Ligands: W11, ZN
Pockets: 12 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 12% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	Human rhinovirus 16 coat protein	protein	285	15% helix, 32% strand	Q82122
2	Human rhinovirus 16 coat protein	protein	252	12% helix, 37% strand	Q82122
3	Human rhinovirus 16 coat protein	protein	238	10% helix, 33% strand	Q82122
4	Human rhinovirus 16 coat protein	protein	29	10% helix, 7% strand	Q82122

Ligands and binding sites

W11 · 3-{3,5-dimethyl-4-[3-(3-methyl-isoxazol-5-yl)-propoxy]-phenyl}-5-trifluoromethyl-[1,2,4]oxadiazole · ligand · chains 1
ZN · Zinc ion · metal · chains 1

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

Pockets

12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	407	0.77	0.86	67	W11
2	204	0.54	0.78	25	empty
3	310	0.54	0.75	40	empty
4	97	0.46	0.80	21	empty
5	91	0.44	0.79	23	empty

Interfaces

5 interfaces between chains.

1–3 · 4274 Å² buried · 64 hydrogen bonds · protein-protein
1–2 · 2127 Å² buried · 40 hydrogen bonds · protein-protein
2–3 · 1703 Å² buried · 18 hydrogen bonds · protein-protein
1–4 · 694 Å² buried · 6 hydrogen bonds · protein-protein
3–4 · 353 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

1C8M · Refined crystal structure of human rhinovirus 16 complexed with VP63843 (pleconaril), an… · 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 Q82122
Elsewhere: RCSB PDB 1C8M · PDBe 1C8M · UniProt Q82122

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