MolNFT v1 · #103344 · protein
A benzonitrile analogue inhibits rhinovirus replication
4PDW · Genome polyprotein: “A benzonitrile analogue inhibits rhinovirus replication”. X-ray diffraction, 1 ligand (2XK), 9 pockets (best druggability 0.79). MolNFT v1 #103344 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4PDW
- Type
- protein
- Length
- 801 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Genome polyprotein; Capsid protein VP4/VP2
- EC
- 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48
- UniProt
- P03303, F5A5A0
- Ligands
- 2XK
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Genome polyprotein (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 274 | 11% helix, 31% strand | P03303 |
| B | Genome polyprotein (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 255 | 15% helix, 37% strand | P03303 |
| C | Genome polyprotein (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 231 | 10% helix, 31% strand | P03303 |
| D | Capsid protein VP4/VP2 | protein | 41 | 17% helix, 2% strand | F5A5A0 |
Ligands and binding sites
- 2XK · 4-[(4,5-dimethoxy-2-nitrophenyl)acetyl]benzonitrile · ligand · chains A, C
- GOL · Glycerol · additive · 4 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 540 | 0.79 | 0.85 | 70 | GOL, 2XK |
| 2 | 193 | 0.49 | 0.76 | 37 | empty |
| 3 | 115 | 0.45 | 0.78 | 32 | empty |
| 4 | 114 | 0.42 | 0.76 | 25 | empty |
| 5 | 75 | 0.38 | 0.78 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–C · 3844 Ų buried · 64 hydrogen bonds · protein-protein
- A–B · 2123 Ų buried · 46 hydrogen bonds · protein-protein
- B–C · 1677 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 968 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 908 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4PDW · A benzonitrile analogue inhibits rhinovirus replication · 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 P03303
- Every structure of UniProt F5A5A0
- Elsewhere: RCSB PDB 4PDW · PDBe 4PDW · UniProt P03303 · UniProt F5A5A0
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