MolNFT v1 · #72613 · protein
HIV-1 protease SAQUINAVIR:RITONAVIR 1:5 complex structure
3NDU: “HIV-1 protease SAQUINAVIR:RITONAVIR 1:5 complex structure”. X-ray diffraction, 4 ligands (ARF, ROC, NA), 4 pockets (best druggability 0.74). MolNFT v1 #72613 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3NDU
- Type
- protein
- Length
- 396 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease
- EC
- 3.4.23.16
- UniProt
- Q7SSI0
- Ligands
- ARF, ROC, NA, CL
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Protease (EC 3.4.23.16) | protein | 99 | 4% helix, 56% strand | Q7SSI0 |
Ligands and binding sites
- ARF · Formamide · ligand · 2 copies · chains A, B
- ROC · (2S)-N-[(2S,3R)-4-[(2S,3S,4aS,8aS)-3-(tert-butylcarbamoyl)-3,4,4a,5,6,7,8,8a-octahydro-1H-isoquinolin-2-yl]-3-hydroxy-1 -phenyl-butan-2-yl]-2-(quinolin-2-ylcarbonylamino)butanediamide · ligand · 2 copies · chains A, B, C, D
- NA · Sodium ion · metal · 3 copies · chains A, B
- CL · Chloride ion · ion · 6 copies · chains A, B, C
- DMS · Dimethyl sulfoxide · additive · 5 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 575 | 0.74 | 0.81 | 51 | ROC, GOL |
| 2 | 390 | 0.71 | 0.82 | 34 | ROC |
| 3 | 112 | 0.39 | 0.75 | 15 | empty |
| 4 | 61 | 0.32 | 0.76 | 14 | ACT |
Interfaces
5 interfaces between chains.
- C–D · 1842 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 1838 Ų buried · 33 hydrogen bonds · protein-protein
- B–D · 292 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 168 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 71 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3NDU · HIV-1 Protease Saquinavir:Ritonavir 1:5 complex structure · the same entry in another collection · chain C against C, 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 Q7SSI0
- Elsewhere: RCSB PDB 3NDU · PDBe 3NDU · UniProt Q7SSI0
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