MolNFT v1 · #140849 · protein
Crystal structure of zika virus NS3 protease in complex with a small molecule inhibitor
5YOD · NS2B cofactor: “Crystal structure of zika virus NS3 protease in complex with a small molecule inhibitor”. X-ray diffraction, 1 ligand (BEZ), 5 pockets (best druggability 0.61). MolNFT v1 #140849 on GenesisL1: 3D structure, binding…
- PDB
- 5YOD
- Type
- protein
- Length
- 755 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NS2B cofactor; NS3 protease
- Ligands
- BEZ
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | NS2B cofactor | protein | 38 | 0% helix, 42% strand | — |
| B, D | NS3 protease | protein | 152 | 5% helix, 45% strand | — |
| F | NS3 protease | protein | 150 | 5% helix, 45% strand | — |
| H | NS3 protease | protein | 149 | 5% helix, 47% strand | — |
Ligands and binding sites
- BEZ · Benzoic acid · ligand · 4 copies · chains B, D, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 366 | 0.61 | 0.77 | 56 | empty |
| 2 | 188 | 0.48 | 0.76 | 27 | empty |
| 3 | 185 | 0.45 | 0.74 | 26 | empty |
| 4 | 124 | 0.42 | 0.76 | 17 | empty |
| 5 | 133 | 0.40 | 0.74 | 19 | empty |
Interfaces
11 interfaces between chains.
- G–H · 2056 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 2033 Ų buried · 33 hydrogen bonds · protein-protein
- E–F · 2028 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 2019 Ų buried · 32 hydrogen bonds · protein-protein
- D–F · 385 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 5YOD · Crystal structure of zika virus NS3 protease in complex with a small molecule inhibitor · the same entry in another collection · chain F against F, 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
- Elsewhere: RCSB PDB 5YOD · PDBe 5YOD
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