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Crystal structure of dengue virus serotype 3 RNA dependent RNA polymerase bound to HEE1-2TYR, a new pyridobenzothizole inhibitor
Analyse Crystal structure of dengue virus serotype 3 RNA dependent RNA polymerase bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IQ6
- Type
- protein
- Length
- 576 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA dependent RNA polymerase
- UniProt
- Q6DLV0
- Ligands
- 6CJ, ZN
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA dependent RNA polymerase | protein | 576 | 50% helix, 10% strand | Q6DLV0 |
Ligands and binding sites
- 6CJ · N-[8-(cyclohexyloxy)-1-oxo-2-phenyl-1H-pyrido[2,1-b][1,3]benzothiazole-4-carbonyl]-L-tyrosine · 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 | 623 | 0.67 | 0.76 | 73 | empty |
| 2 | 75 | 0.46 | 0.82 | 18 | empty |
| 3 | 59 | 0.41 | 0.81 | 16 | empty |
| 4 | 113 | 0.41 | 0.76 | 21 | empty |
| 5 | 62 | 0.36 | 0.78 | 17 | empty |
Compared structures
- 5IQ6 · Crystal structure of Dengue virus serotype 3 RNA dependent RNA polymerase bound to… · 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 5IQ6 · PDBe 5IQ6 · UniProt Q6DLV0
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