Structure of PDB 4rda Chain B Binding Site BS03

Receptor Information

>4rda Chain B (length=196) Species: 9606 (Homo sapiens)

DGVDIYFGMPGEISEHEGFLRAKMDLEERRMRQINEVMREWAMADNQSKN
LPKADRQALNEHFQSILQTLEEQVSGERQRLVETHATRVIALINDQRRAA
LEGFLAALQADPPQAERVLLALRRYLRAEQKEQRHTLRHYQHVAAVDPEK
AQQMRFQVHTHLQVIEERVNQSLGLLDQNPHLAQELRPQIQELLHS

Ligand information

• Ligand ID: SGN
• InChI: InChI=1S/C6H13NO11S2/c8-4-2(1-17-20(14,15)16)18-6(10)3(5(4)9)7-19(11,12)13/h2-10H,1H2,(H,11,12,13)(H,14,15,16)/t2-,3-,4-,5-,6+/m1/s1
• InChIKey: DQTRACMFIGDHSN-UKFBFLRUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O)NS(=O)(=O)O)O)O)OS(=O)(=O)O
  CACTVS 3.341: O[CH]1O[CH](CO[S](O)(=O)=O)[CH](O)[CH](O)[CH]1N[S](O)(=O)=O
  OpenEye OEToolkits 1.5.0: C(C1C(C(C(C(O1)O)NS(=O)(=O)O)O)O)OS(=O)(=O)O
  ACDLabs 10.04: O=S(=O)(O)OCC1OC(O)C(NS(=O)(=O)O)C(O)C1O
  CACTVS 3.341: O[C@H]1O[C@H](CO[S](O)(=O)=O)[C@@H](O)[C@H](O)[C@H]1N[S](O)(=O)=O
• Formula: C6 H13 N O11 S2
• Name: 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose;
  N,O6-DISULFO-GLUCOSAMINE;
  6-O-sulfo-N-sulfo-alpha-D-glucosamine;
  2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucose;
  2-deoxy-6-O-sulfo-2-(sulfoamino)-D-glucose;
  2-deoxy-6-O-sulfo-2-(sulfoamino)-glucose
• DrugBank: DB03959
• PDB chain: 4rda Chain D Residue 6

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4rda Interaction of the amyloid precursor protein-like protein 1 (APLP1) E2 domain with heparan sulfate involves two distinct binding modes.
• Resolution: 2.497 Å
• Binding residue (original residue number in PDB): R429 H430 H433
• Binding residue (residue number reindexed from 1): R138 H139 H142
• Annotation score: 4

Gene Ontology

Cellular Component

• GO:0016020 membrane

External links

• PDB: RCSB:4rda, PDBe:4rda, PDBj:4rda
• PDBsum: 4rda
• PubMed: 25760599
• UniProt: P51693|APLP1_HUMAN Amyloid beta precursor like protein 1 (Gene Name=APLP1)