MolNFT v1 · #125546 · protein
Crystal structure of zika virus NS2B-NS3 protease in complex with a boronate inhibitor
5LC0 · NS2B-NS3 PROTEASE,NS2B-NS3 protease: “Crystal structure of zika virus NS2B-NS3 protease in complex with a boronate inhibitor”. X-ray diffraction, 1 ligand (6T8), 5 pockets (best druggability 0.84). MolNFT v1 #125546 on GenesisL1: 3D…
- PDB
- 5LC0
- Type
- protein
- Length
- 383 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NS2B-NS3 PROTEASE,NS2B-NS3 protease
- UniProt
- A0A140FB25, A0A140DLX4
- Ligands
- 6T8
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NS2B-NS3 PROTEASE,NS2B-NS3 protease | protein | 193 | 2% helix, 45% strand | A0A140FB25, A0A140DLX4 |
| B | NS2B-NS3 PROTEASE,NS2B-NS3 protease | protein | 190 | 2% helix, 43% strand | A0A140FB25, A0A140DLX4 |
Ligands and binding sites
- 6T8 · N-((S)-3-(4-(aminomethyl)phenyl)-1-(((R)-4-guanidino-1-(5-hydroxy-1,3,2-dioxaborinan-2-yl)butyl)amino)-1-oxopropan-2-yl)benzamide · ligand · 2 copies · chains A, B
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 | 956 | 0.84 | 0.86 | 81 | 6T8 |
| 2 | 166 | 0.47 | 0.76 | 21 | empty |
| 3 | 112 | 0.39 | 0.75 | 20 | empty |
| 4 | 66 | 0.34 | 0.76 | 16 | empty |
| 5 | 54 | 0.26 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1197 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5LC0 · Crystal structure of Zika virus NS2B-NS3 protease in complex with a boronate inhibitor · 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 A0A140FB25
- Every structure of UniProt A0A140DLX4
- Elsewhere: RCSB PDB 5LC0 · PDBe 5LC0 · UniProt A0A140FB25 · UniProt A0A140DLX4
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