Research workbench
OYE1 W116A complexed with (Z)-methyl 3-cyano-3-(4-fluorophenyl) acrylate in a non productive binding mode
Analyse OYE1 W116A complexed with (Z)-methyl 3-cyano-3-(4-fluorophenyl) acrylate in a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YIL
- Type
- protein
- Length
- 397 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADPH dehydrogenase 1
- EC
- 1.6.99.1
- UniProt
- Q02899
- Ligands
- FMN, 4D3, MG, NA
- Pockets
- 1 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NADPH dehydrogenase 1 (EC 1.6.99.1) | protein | 397 | 37% helix, 14% strand | Q02899 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · chains A
- 4D3 · methyl (2Z)-3-cyano-3-(4-fluorophenyl)prop-2-enoate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 305 | 0.83 | 0.93 | 47 | FMN, 4D3 |
Compared structures
- 4YIL · OYE1 W116A complexed with (Z)-methyl 3-cyano-3-(4-FLUOROPHENYL)ACRYLATE in a non… · the same entry in another collection · chain A against A, TM-score 1.00
- Q02899 · AlphaFold monomer V2.0 prediction for NADPH dehydrogenase 1 (Q02899) · a predicted model of the same protein · 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 Q02899
- Elsewhere: RCSB PDB 4YIL · PDBe 4YIL · UniProt Q02899
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