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DDR1, 3-[2-(6-aminopyridin-3-YL)ETHYNYL]-N-[3-(trifluoromethyl) PHENYL]BENZAMIDE, 1.800A, P212121, RFREE=23.1%

Analyse DDR1, 3-[2-(6-aminopyridin-3-YL)ETHYNYL]-N-[3-(trifluoromethyl)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
5SAU
Type
protein
Length
287 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
1IF
Pockets
1 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 17% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AEpithelial discoidin domain-containing receptor 1 (EC 2.7.10.1)protein28741% helix, 17% strandQ08345

Ligands and binding sites

  • 1IF · 3-[(6-aminopyridin-3-yl)ethynyl]-N-[3-(trifluoromethyl)phenyl]benzamide · ligand · chains A
  • MLI · Malonate ion · additive · 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.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
13840.740.85551IF

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

  • 5SAU · DDR1, 3-[2-(6-aminopyridin-3-yl)ethynyl]-N-[3-(trifluoromethyl)phenyl]benzamide, 1.800A… · 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 0.95

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