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Structure-based design of a novel series of azetidine inhibitors of the hepatitis C virus NS3/4A serine protease

Analyse Structure-based design of a novel series of azetidine inhibitors of the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4TYD
Type: protein
Length: 2,321 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NS3 protease
UniProt: Q0ZNA6
Ligands: 3EO, ZN, CL
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 9 distinct chains · 14% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	NS3 protease	protein	194	14% helix, 45% strand	Q0ZNA6
B, J	NS3 protease	protein	196	15% helix, 46% strand	Q0ZNA6
C	NS3 protease	protein	196	14% helix, 46% strand	Q0ZNA6
D	NS3 protease	protein	195	16% helix, 47% strand	Q0ZNA6
E, G	NS3 protease	protein	190	12% helix, 47% strand	Q0ZNA6
F, M	NS3 protease	protein	195	14% helix, 46% strand	Q0ZNA6
H	NS3 protease	protein	193	16% helix, 46% strand	Q0ZNA6
K	NS3 protease	protein	194	13% helix, 47% strand	Q0ZNA6
L	NS3 protease	protein	187	11% helix, 49% strand	Q0ZNA6

Ligands and binding sites

3EO · (4R,6S,7Z,15S,17S)-17-[({7-methoxy-2-[4-(propan-2-yl)-1,3-thiazol-2-yl]quinolin-4-yl}oxy)methyl]-13-methyl-N-[(1-methylcyclopropyl)sulfonyl]-2,14-dioxo-1,3,13-triazatricyclo[13.2.0.0~4,6~]heptadec-7-ene-4-carboxamide · ligand · 12 copies · chains A, D, B, E, C, F, G, M, H, J, L, K
ZN · Zinc ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, J, K, L, M
CL · Chloride ion · ion · 11 copies · chains A, B, C, E, D, F, G, H, M

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

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	430	0.82	0.90	78	CL
2	747	0.81	0.84	84	empty
3	466	0.81	0.88	64	empty
4	460	0.79	0.87	74	empty
5	359	0.74	0.86	56	empty

Interfaces

25 interfaces between chains.

C–F · 470 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 465 Å² buried · 2 hydrogen bonds · protein-protein
G–H · 458 Å² buried · 1 hydrogen bond · protein-protein
A–F · 418 Å² buried · 1 hydrogen bond · protein-protein
C–E · 416 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

4TYD · Structure-based design of a novel series of azetidine inhibitors of the hepatitis C virus… · the same entry in another collection · chain A against A, 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 Q0ZNA6
Elsewhere: RCSB PDB 4TYD · PDBe 4TYD · UniProt Q0ZNA6

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