MolNFT v1 · #119408 · protein
Human FEN1 in complex with an N-hydroxyurea compound
5FV7 · Flap endonuclease 1: “Human FEN1 in complex with an N-hydroxyurea compound”. X-ray diffraction, 2 ligands (R3Z, MG), 4 pockets (best druggability 0.66). MolNFT v1 #119408 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5FV7
- Type
- protein
- Length
- 557 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Flap endonuclease 1
- EC
- 3.1.-.-
- UniProt
- P39748
- Ligands
- R3Z, MG
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Flap endonuclease 1 (EC 3.1.-.-) | protein | 283 | 49% helix, 11% strand | P39748 |
| B | Flap endonuclease 1 (EC 3.1.-.-) | protein | 274 | 51% helix, 11% strand | P39748 |
Ligands and binding sites
- R3Z · 1-[(2S)-2,3-dihydro-1,4-benzodioxin-2-ylmethyl]-3-hydroxythieno[3,2-d]pyrimidine-2,4(1H,3H)-dione · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 692 | 0.66 | 0.75 | 58 | empty |
| 2 | 50 | 0.46 | 0.85 | 15 | empty |
| 3 | 115 | 0.40 | 0.75 | 19 | MG, R3Z |
| 4 | 107 | 0.36 | 0.74 | 18 | MG, R3Z |
Interfaces
1 interface between chains.
- A–B · 169 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
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 P39748
- Elsewhere: RCSB PDB 5FV7 · PDBe 5FV7 · UniProt P39748
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