MolNFT v1 · #9299 · protein

HRV14/SDZ 35-682 complex

1HRV · Human rhinovirus 14 coat protein (subunit VP1): “HRV14/SDZ 35-682 complex”. X-ray diffraction, 1 ligand (SDZ), 9 pockets (best druggability 0.83). MolNFT v1 #9299 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1HRV
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: SDZ
Pockets: 9 · best druggability 0.83

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	Human rhinovirus 14 coat protein (subunit VP1)	protein	273	10% helix, 32% 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

SDZ · 1-[2-hydroxy-3-(4-cyclohexyl-phenoxy)-propyl]-4-(2-pyridyl)-piperazine · 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	586	0.83	0.88	81	SDZ
2	168	0.46	0.76	34	empty
3	92	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 · 4152 Å² buried · 72 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 · 957 Å² buried · 14 hydrogen bonds · protein-protein
3–4 · 898 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

1HRV · HRV14/SDZ 35-682 complex · 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 1HRV · PDBe 1HRV · UniProt P03303

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