MolNFT v1 · #94651 · protein
Crystal structure of HCV NS3/4A D168V protease complexed with compound 4
4I32 · Genome polyprotein: “Crystal structure of HCV NS3/4A D168V protease complexed with compound 4”. X-ray diffraction, 2 ligands (1BV, NA), 4 pockets (best druggability 0.33). MolNFT v1 #94651 on GenesisL1: 3D structure, binding sites…
- PDB
- 4I32
- Type
- protein
- Length
- 390 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Genome polyprotein; HCV non-structural protein 4A
- EC
- 3.4.22.-, 3.4.21.98, 3.6.1.15, 3.6.4.13, 2.7.7.48
- UniProt
- P26662
- Ligands
- 1BV, NA
- Pockets
- 4 · best druggability 0.33
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Genome polyprotein (EC 3.4.22.-, 3.4.21.98, 3.6.1.15, 3.6.4.13, 2.7.7.48) | protein | 182 | 15% helix, 43% strand | P26662 |
| C, D | HCV non-structural protein 4A | protein | 13 | 0% helix, 69% strand | P26662 |
Ligands and binding sites
- 1BV · (2R,6S,7E,10E,13aR,14aR,16aS)-2-{[7-methoxy-8-methyl-2-(propan-2-yloxy)quinolin-4-yl]oxy}-N-[(1-methylcyclopropyl)sulfonyl]-6-{[(1-methyl-1H-pyrazol-3-yl)carbonyl]amino}-5,16-dioxo-1,2,3,6,9,12,13,13a,14,15,16,16a-dodecahydrocyclopropa[e]pyrrolo[1,2-a][1,4]diazacyclopentadecine-14a(5H)-carboxamide · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 54 | 0.33 | 0.78 | 16 | empty |
| 2 | 61 | 0.30 | 0.75 | 20 | empty |
| 3 | 58 | 0.29 | 0.75 | 18 | empty |
| 4 | 50 | 0.25 | 0.73 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1236 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 1223 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 449 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4I32 · Crystal structure of HCV NS3/4A D168V protease complexed with compound 4 · 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 P26662
- Elsewhere: RCSB PDB 4I32 · PDBe 4I32 · UniProt P26662
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