MolNFT v1 · #74857 · protein
Dengue methyltransferase bound to a SAM-based inhibitor
3P8Z · Non-structural protein 5: “Dengue methyltransferase bound to a SAM-based inhibitor”. X-ray diffraction, 2 ligands (36A, SAH), 4 pockets (best druggability 0.67). MolNFT v1 #74857 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3P8Z
- Type
- protein
- Length
- 513 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-structural protein 5
- EC
- 2.1.1.56, 2.1.1.57
- UniProt
- C1KBQ3
- Ligands
- 36A, SAH
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Non-structural protein 5 (EC 2.1.1.56, 2.1.1.57) | protein | 257 | 36% helix, 16% strand | C1KBQ3 |
| C | Non-structural protein 5 (EC 2.1.1.56, 2.1.1.57) | protein | 256 | 37% helix, 16% strand | C1KBQ3 |
Ligands and binding sites
- 36A · (S)-2-amino-4-(((2S,3S,4R,5R)-5-(6-(3-chlorobenzylamino)-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methylthio)butanoic acid · ligand · chains A
- SAH · S-adenosyl-L-homocysteine · ligand · chains 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 539 | 0.67 | 0.78 | 51 | 36A |
| 2 | 571 | 0.66 | 0.77 | 57 | SAH |
| 3 | 58 | 0.39 | 0.80 | 18 | empty |
| 4 | 107 | 0.36 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–C · 536 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3P8Z · Dengue Methyltransferase bound to a SAM-based inhibitor · the same entry in another collection · chain C against C, 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 C1KBQ3
- Elsewhere: RCSB PDB 3P8Z · PDBe 3P8Z · UniProt C1KBQ3
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