Structure of PDB 3qmk Chain A Binding Site BS01

Receptor Information

>3qmk Chain A (length=195) Species: 9606 (Homo sapiens)

DGVDIYFGMPGEISEHEGFLRAKMDLEERRMRQINEVMREWAMADNQSKN
LPKADRQALNEHFQSILQTLEEQVSGERQRLVETHATRVIALINDQRRAA
LEGFLAALQADPPQAERVLLALRRYLRAEQKEQRHTLRHYQHVAAVDPEK
AQQMRFQVHTHLQVIEERVNQSLGLLDQNPHLAQELRPQIQELLH

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: 3qmk Chain C Residue 1

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3qmk Crystal structure of amyloid precursor-like protein 1 and heparin complex suggests a dual role of heparin in E2 dimerization.
• Resolution: 2.21 Å
• Binding residue (original residue number in PDB): H307 K422
• Binding residue (residue number reindexed from 1): H16 K131
• Annotation score: 4
• Binding affinity: PDBbind-CN: -logKd/Ki=6.10,Kd=0.787uM

Gene Ontology

Cellular Component

• GO:0016020 membrane

External links

• PDB: RCSB:3qmk, PDBe:3qmk, PDBj:3qmk
• PDBsum: 3qmk
• PubMed: 21930949
• UniProt: P51693|APLP1_HUMAN Amyloid beta precursor like protein 1 (Gene Name=APLP1)