MolNFT v1 · #76661 · protein
HIV-1 protease (mutant Q7K L33I L63I) in complex with a three-armed pyrrolidine-based inhibitor
3QRM: “HIV-1 protease (mutant Q7K L33I L63I) in complex with a three-armed pyrrolidine-based inhibitor”. X-ray diffraction, 2 ligands (NK7, CL), 1 pocket (best druggability 0.75). MolNFT v1 #76661 on GenesisL1: 3D structure, binding sites…
- PDB
- 3QRM
- Type
- protein
- Length
- 198 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease
- EC
- 3.4.23.16
- UniProt
- P03367
- Ligands
- NK7, CL
- Pockets
- 1 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protease (EC 3.4.23.16) | protein | 99 | 7% helix, 56% strand | P03367 |
Ligands and binding sites
- NK7 · 4-{[4-(trifluoromethyl)benzyl][(3S,4S)-4-{[4-(trifluoromethyl)benzyl]amino}pyrrolidin-3-yl]sulfamoyl}benzamide · ligand · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- DTD · Dithiane diol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 388 | 0.75 | 0.85 | 33 | NK7, DTD |
Interfaces
1 interface between chains.
- A–B · 1848 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 3QRM · HIV-1 protease (mutant Q7K L33I L63I) in complex with a three-armed pyrrolidine-based… · 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 P03367
- Elsewhere: RCSB PDB 3QRM · PDBe 3QRM · UniProt P03367
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