MolNFT v1 · #121718 · protein
Dengue serotype 3 RNA-dependent RNA polymerase bound to compound 27
5I3P · Genome polyprotein: “Dengue serotype 3 RNA-dependent RNA polymerase bound to compound 27”. X-ray diffraction, 2 ligands (68T, ZN), 5 pockets (best druggability 0.70). MolNFT v1 #121718 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5I3P
- Type
- protein
- Length
- 585 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Genome polyprotein
- UniProt
- Q6DLV0
- Ligands
- 68T, ZN
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Genome polyprotein | protein | 585 | 51% helix, 9% strand | Q6DLV0 |
Ligands and binding sites
- 68T · 5-[5-(3-hydroxyprop-1-yn-1-yl)thiophen-2-yl]-2,4-dimethoxy-N-[(3-methoxyphenyl)sulfonyl]benzamide · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 828 | 0.70 | 0.76 | 69 | 68T |
| 2 | 170 | 0.48 | 0.77 | 26 | empty |
| 3 | 105 | 0.46 | 0.79 | 23 | empty |
| 4 | 57 | 0.43 | 0.83 | 16 | empty |
| 5 | 51 | 0.26 | 0.74 | 16 | empty |
Compared structures
- 5I3P · Dengue serotype 3 RNA-dependent RNA polymerase bound to compound 27 · 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 Q6DLV0
- Elsewhere: RCSB PDB 5I3P · PDBe 5I3P · UniProt Q6DLV0
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