MolNFT v1 · #123707 · protein
Crystal structure of SPINDLIN1 bound to compound EML631
5JSJ · Spindlin-1: “Crystal structure of SPINDLIN1 bound to compound EML631”. X-ray diffraction, 3 ligands (6PD, MG, CL), 8 pockets (best druggability 0.53). MolNFT v1 #123707 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5JSJ
- Type
- protein
- Length
- 391 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spindlin-1
- UniProt
- Q9Y657
- Ligands
- 6PD, MG, CL
- Pockets
- 8 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spindlin-1 | protein | 195 | 7% helix, 46% strand | Q9Y657 |
| B | Spindlin-1 | protein | 196 | 7% helix, 47% strand | Q9Y657 |
Ligands and binding sites
- 6PD · [4-(2-pyrrolidin-1-ylethyl)piperidin-1-yl]-[4-[4-(2-pyrrolidin-1-ylethyl)piperidin-1-yl]carbonyl-3-[[4-(pyrrolidin-1-ylmethoxy)phenyl]amino]phenyl]methanone · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.53 | 0.81 | 21 | MG, CL |
| 2 | 65 | 0.48 | 0.83 | 10 | empty |
| 3 | 58 | 0.40 | 0.80 | 8 | empty |
| 4 | 58 | 0.39 | 0.80 | 18 | empty |
| 5 | 102 | 0.37 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 213 Ų buried · 7 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 Q9Y657
- Elsewhere: RCSB PDB 5JSJ · PDBe 5JSJ · UniProt Q9Y657
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