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Crystal structure of vaccinia virus decapping enzyme D9 in complex with inhibitor CP100356
Analyse Crystal structure of vaccinia virus decapping enzyme D9 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7T7H
- Type
- protein
- Length
- 399 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA repair ntp-phosphohydrolase
- UniProt
- L7QJE0
- Ligands
- G7R, NA
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA repair ntp-phosphohydrolase | protein | 204 | 27% helix, 31% strand | L7QJE0 |
| B | DNA repair ntp-phosphohydrolase | protein | 195 | 27% helix, 34% strand | L7QJE0 |
Ligands and binding sites
- G7R · 4-(6,7-dimethoxy-3,4-dihydroisoquinolin-2(1H)-yl)-N-[2-(3,4-dimethoxyphenyl)ethyl]-6,7-dimethoxyquinazolin-2-amine · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 915 | 0.79 | 0.81 | 87 | G7R |
| 2 | 333 | 0.71 | 0.84 | 39 | G7R |
| 3 | 74 | 0.41 | 0.79 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 600 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7T7H · Crystal structure of Vaccinia Virus decapping enzyme D9 in complex with inhibitor CP100356 · 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 L7QJE0
- Elsewhere: RCSB PDB 7T7H · PDBe 7T7H · UniProt L7QJE0
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