MolNFT v1 · #69096 · protein
HIV protease (pr) with inhibitor tl-3 bound, and dmsos in exo site
3KFP: “HIV protease (pr) with inhibitor tl-3 bound, and dmsos in exo site”. X-ray diffraction, 1 ligand (3TL), 2 pockets (best druggability 0.50). MolNFT v1 #69096 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3KFP
- Type
- protein
- Length
- 99 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease
- EC
- 3.4.23.16
- UniProt
- Q903N5
- Ligands
- 3TL
- Pockets
- 2 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protease (EC 3.4.23.16) | protein | 99 | 4% helix, 48% strand | Q903N5 |
Ligands and binding sites
- 3TL · benzyl [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-dibenzyl-8,9-dihydroxy-1,16-dimethyl-4,13-bis(1-methylethyl)-2,5,12,15,18-pentaoxo-20-phenyl-19-oxa-3,6,11,14,17-pentaazaicos-1-yl]carbamate · ligand · chains A
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A
- BME · Beta-mercaptoethanol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 163 | 0.50 | 0.77 | 21 | empty |
| 2 | 80 | 0.31 | 0.74 | 18 | empty |
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 3KFP · HIV Protease (PR) with inhibitor TL-3 bound, and DMSOs in exo site · 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 Q903N5
- Elsewhere: RCSB PDB 3KFP · PDBe 3KFP · UniProt Q903N5
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