MolNFT v1 · #138696 · protein
Hepatitis B virus core protein Y132A mutant in complex with heteroaryldihydropyrimidine (HAP_R01)
5WRE: “Hepatitis B virus core protein Y132A mutant in complex with heteroaryldihydropyrimidine (HAP_R01)”. X-ray diffraction, 2 ligands (7TL, CL), 11 pockets (best druggability 0.72). MolNFT v1 #138696 on GenesisL1: 3D structure, binding…
- PDB
- 5WRE
- Type
- protein
- Length
- 868 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Core protein
- UniProt
- L7R9I1
- Ligands
- 7TL, CL
- Pockets
- 11 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 69% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E | Core protein | protein | 142 | 71% helix, 0% strand | L7R9I1 |
| D | Core protein | protein | 150 | 69% helix, 0% strand | L7R9I1 |
| F | Core protein | protein | 150 | 67% helix, 0% strand | L7R9I1 |
Ligands and binding sites
- 7TL · (2S)-1-[[(4R)-4-(2-chloranyl-4-fluoranyl-phenyl)-5-methoxycarbonyl-2-(1,3-thiazol-2-yl)-1,4-dihydropyrimidin-6-yl]methyl]-4,4-bis(fluoranyl) pyrrolidine-2-carboxylic acid · ligand · 6 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 3 copies · chains A, B, D
- IPA · Isopropyl alcohol · additive · 7 copies · chains A, B, F, C, D, E
- GOL · Glycerol · additive · 6 copies · chains B, C, D, E, F, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 270 | 0.72 | 0.86 | 29 | 7TL |
| 2 | 270 | 0.69 | 0.84 | 30 | 7TL |
| 3 | 277 | 0.69 | 0.84 | 30 | 7TL |
| 4 | 117 | 0.55 | 0.83 | 32 | IPA |
| 5 | 86 | 0.42 | 0.79 | 16 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1993 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1993 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1965 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 496 Ų buried · 2 hydrogen bonds · protein-protein
- A–F · 483 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5WRE · Hepatitis B virus core protein Y132A mutant in complex with heteroaryldihydropyrimidine… · 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 L7R9I1
- Elsewhere: RCSB PDB 5WRE · PDBe 5WRE · UniProt L7R9I1
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