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MolNFT v1 · #133796 · protein

DDR1, 4-chloro-N-[(3S,4R)-4-phenylpyrrolidin-3-yl]-3-(1H-PYRROLO[2,3- B]PYRIDIN-5-YLOXYMETHYL)BENZAMIDE, 1.530A, P212121, RFREE=21.4%

5SB1 · Epithelial discoidin domain-containing receptor 1: “DDR1, 4-chloro-N-[(3S,4R)-4-phenylpyrrolidin-3-yl]-3-(1H-PYRROLO[2,3- B]PYRIDIN-5-YLOXYMETHYL)BENZAMIDE…”. X-ray diffraction, 2 ligands (1JI, SO4), 1 pocket (best druggability…

PDB
5SB1
Type
protein
Length
284 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
1JI, SO4
Pockets
1 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 17% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AEpithelial discoidin domain-containing receptor 1 (EC 2.7.10.1)protein28442% helix, 17% strandQ08345

Ligands and binding sites

  • 1JI · 4-chloro-N-[(3S,4R)-4-phenylpyrrolidin-3-yl]-3-{[(1H-pyrrolo[2,3-b]pyridin-5-yl)oxy]methyl}benzamide · ligand · chains A
  • SO4 · Sulfate ion · ion · 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
15190.740.82491JI

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

  • 5SB1 · DDR1, 4-chloro-N-[(3S,4R)-4-phenylpyrrolidin-3-yl]-3-(1H-pyrrolo[2,3-b]pyridin-5-yloxymeth… · 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 0.97

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