MolNFT v1 · #143560 · protein
Crystal structure of HIV protease complexed with N-(3-fluoro-2-(2- ((2S,6R)-6-methyl-1-(PHENYLSULFONYL)PIPERAZIN-2-YL)ETHYL)PHENYL)-3,3- BIS(4-FLUOROPHENYL)PROPANAMIDE
6B38 · HIV-1 protease: “Crystal structure of HIV protease complexed with N-(3-fluoro-2-(2…”. X-ray diffraction, 2 ligands (CKM, CL), 1 pocket (best druggability 0.72). MolNFT v1 #143560 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6B38
- Type
- protein
- Length
- 198 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 protease
- EC
- 3.4.23.16
- UniProt
- P04587
- Ligands
- CKM, CL
- Pockets
- 1 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | HIV-1 protease (EC 3.4.23.16) | protein | 99 | 7% helix, 55% strand | P04587 |
Ligands and binding sites
- CKM · N-(3-fluoro-2-{2-[(2S,6R)-6-methyl-1-(phenylsulfonyl) piperazin-2-yl]ethyl}phenyl)-3,3-bis(4-fluorophenyl) propanamide · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · 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 | 410 | 0.72 | 0.83 | 41 | CKM |
Interfaces
1 interface between chains.
- A–B · 1866 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- 6B38 · Crystal Structure of HIV Protease complexed with… · 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 P04587
- Elsewhere: RCSB PDB 6B38 · PDBe 6B38 · UniProt P04587
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