MolNFT v1 · #148845 · protein
DDR1, 2-[1'-(1H-indazole-5-carbonyl)-4-methyl-2-OXOSPIRO[INDOLE-3,4'- piperidine]-1-yl]-N-(2,2,2-TRIFLUOROETHYL)ACETAMIDE, 1.990A, P6522, RFREE=27.7%
6FIO · Epithelial discoidin domain-containing receptor 1: “DDR1, 2-[1'-(1H-indazole-5-carbonyl)-4-methyl-2-OXOSPIRO[INDOLE-3,4'…”. X-ray diffraction, 1 ligand (DJH), 3 pockets (best druggability 0.74). MolNFT v1 #148845 on GenesisL1: 3D…
- PDB
- 6FIO
- Type
- protein
- Length
- 307 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epithelial discoidin domain-containing receptor 1
- EC
- 2.7.10.1
- UniProt
- Q08345
- Ligands
- DJH
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epithelial discoidin domain-containing receptor 1 (EC 2.7.10.1) | protein | 307 | 40% helix, 16% strand | Q08345 |
Ligands and binding sites
- DJH · 2-[1'-(1~{H}-indazol-5-ylcarbonyl)-4-methyl-2-oxidanylidene-spiro[indole-3,4'-piperidine]-1-yl]-~{N}-[2,2,2-tris(fluoranyl)ethyl]ethanamide · ligand · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 542 | 0.74 | 0.81 | 54 | DJH |
| 2 | 131 | 0.45 | 0.77 | 22 | empty |
| 3 | 76 | 0.31 | 0.74 | 18 | empty |
Compared structures
- 6FIO · DDR1, 2-[1'-(1H-indazole-5-carbonyl)-4-methyl-2-oxospiro[indole-3,4'-piperidine]-1-yl]-N-(… · the same entry in another collection · chain A against A, TM-score 1.00
- Q08345 · AlphaFold monomer V2.0 prediction for epithelial discoidin domain- containing receptor 1… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q08345
- Elsewhere: RCSB PDB 6FIO · PDBe 6FIO · UniProt Q08345
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