MolNFT v1 · #186696 · protein
Disulfide stabilized HIV-1 ca hexamer in complex with capsid inhibitor (S)-N-(1-(3-(4-chloro-3-(methylsulfonamido)-1-(2,2,2-trifluoroethyl)- 1H-indazol-7-yl)-6-(3-methyl-3-(METHYLSULFONYL)BUT-1-yn-1-YL)PYRIDIN- 2-yl)-2-(3,5-DIFLUOROPHENYL)ETHYL)-2-(3-(trifluoromethyl)-4,5,6,7- tetrahydro-1H-indazol-1-YL)ACETAMIDE
7RMJ · Capsid protein P24: “Disulfide stabilized HIV-1 ca hexamer in complex with capsid inhibitor…”. X-ray diffraction, 3 ligands (61F, CL, IOD), 4 pockets (best druggability 0.34). MolNFT v1 #186696 on GenesisL1: 3D structure, binding…
- PDB
- 7RMJ
- Type
- protein
- Length
- 657 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein P24
- UniProt
- B6DRA0
- Ligands
- 61F, CL, IOD
- Pockets
- 4 · best druggability 0.34
Structure
x-ray diffraction · 3 distinct chains · 59% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein P24 | protein | 219 | 59% helix, 3% strand | B6DRA0 |
| B | Capsid protein P24 | protein | 218 | 59% helix, 3% strand | B6DRA0 |
| C | Capsid protein P24 | protein | 220 | 58% helix, 3% strand | B6DRA0 |
Ligands and binding sites
- 61F · N-[(1S)-1-(3-{4-chloro-3-[(methanesulfonyl)amino]-1-(2, 2,2-trifluoroethyl)-1H-indazol-7-yl}-6-[3-(methanesulfonyl)-3-methylbut-1-yn-1-yl]pyridin-2-yl)-2-(3,5-difluorophenyl)ethyl]-2-[3-(trifluoromethyl)-4, 5,6,7-tetrahydro-1H-indazol-1-yl]acetamide · ligand · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 17 copies · chains A, B, C
- IOD · Iodide ion · ion · 5 copies · chains A, B, 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.34 | 0.76 | 17 | empty |
| 2 | 66 | 0.33 | 0.76 | 14 | empty |
| 3 | 73 | 0.33 | 0.75 | 14 | empty |
| 4 | 55 | 0.29 | 0.75 | 14 | empty |
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7RMJ · Disulfide stabilized HIV-1 CA hexamer in complex with capsid inhibitor… · 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 B6DRA0
- Elsewhere: RCSB PDB 7RMJ · PDBe 7RMJ · UniProt B6DRA0
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