MolNFT v1 · #25439 · protein

HRV14/SDZ 880-061 complex

1VRH · Rhinovirus 14: “HRV14/SDZ 880-061 complex”. X-ray diffraction, 1 ligand (SD8), 11 pockets (best druggability 0.82). MolNFT v1 #25439 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1VRH
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: SD8
Pockets: 11 · best druggability 0.82

Structure

x-ray diffraction · 4 distinct chains · 12% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	Rhinovirus 14	protein	273	11% helix, 30% 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

SD8 · 2-[4-(2H-1,4-benzothiazine-3-yl)-piperazine-1-ly]-1,3-thiazole-4-carboxylic acid ethylester · ligand · chains 1

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

Pockets

11 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	381	0.82	0.91	39	SD8
2	173	0.50	0.77	35	empty
3	167	0.46	0.76	34	empty
4	92	0.42	0.78	18	empty
5	110	0.40	0.76	21	empty

Interfaces

6 interfaces between chains.

1–3 · 4158 Å² buried · 71 hydrogen bonds · protein-protein
1–2 · 2096 Å² buried · 44 hydrogen bonds · protein-protein
2–3 · 1705 Å² buried · 15 hydrogen bonds · protein-protein
1–4 · 960 Å² buried · 14 hydrogen bonds · protein-protein
3–4 · 896 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

1VRH · HRV14/SDZ 880-061 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 1VRH · PDBe 1VRH · UniProt P03303

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