MolNFT v1 · #136824 · protein
X-ray crystal structure of wild type HIV-1 protease in complex with grl-09510
5V4Y: “X-ray crystal structure of wild type HIV-1 protease in complex with grl-09510”. X-ray diffraction, 1 ligand (8FM), 2 pockets (best druggability 0.45). MolNFT v1 #136824 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5V4Y
- Type
- protein
- Length
- 99 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease
- UniProt
- Q72874
- Ligands
- 8FM
- Pockets
- 2 · best druggability 0.45
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protease | protein | 99 | 7% helix, 48% strand | Q72874 |
Ligands and binding sites
- 8FM · (3S,3aR,5R,7aS,8S)-hexahydro-4H-3,5-methanofuro[2,3-b]pyran-8-yl [(2S,3R)-3-hydroxy-4-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}-1-phenylbutan-2-yl]carbamate · ligand · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 185 | 0.45 | 0.74 | 22 | empty |
| 2 | 79 | 0.32 | 0.74 | 19 | empty |
Compared structures
- 5V4Y · X-ray crystal structure of wild type HIV-1 protease in complex with GRL-09510 · 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 Q72874
- Elsewhere: RCSB PDB 5V4Y · PDBe 5V4Y · UniProt Q72874
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