Structure of PDB 2rid Chain C Binding Site BS04

Receptor Information

>2rid Chain C (length=149) Species: 9606 (Homo sapiens)

LRQQVEALQGQVQHLQAAFSQYKKVELFPNGQSVGEKIFKTAGFVKPFTE
AQLLCTQAGGQLASPRSAAENAALQQLVVAKNEAAFLSMTDSKTEGKFTY
PTGESLVYSNWAPGEPNDDGGSEDCVEIFTNGKWNDRACGEKRLVVCEF

Ligand information

• Ligand ID: 291
• InChI: InChI=1S/C11H19NO8/c1-2-3-18-10-8(16)6(14)7(15)9(20-10)5(13)4-19-11(12)17/h2,5-10,13-16H,1,3-4H2,(H2,12,17)/t5-,6-,7-,8-,9+,10-/m0/s1
• InChIKey: JSAVYXHOFSIYSH-UCKHGQTESA-N
• SMILES:
  CACTVS 3.341: NC(=O)OC[CH](O)[CH]1O[CH](OCC=C)[CH](O)[CH](O)[CH]1O
  OpenEye OEToolkits 1.5.0: C=CCOC1C(C(C(C(O1)C(COC(=O)N)O)O)O)O
  ACDLabs 10.04: O=C(OCC(O)C1OC(OC/C=C)C(O)C(O)C1O)N
  CACTVS 3.341: NC(=O)OC[C@H](O)[C@H]1O[C@H](OCC=C)[C@@H](O)[C@@H](O)[C@@H]1O
  OpenEye OEToolkits 1.5.0: C=CCO[C@@H]1[C@H]([C@H]([C@@H]([C@H](O1)[C@H](COC(=O)N)O)O)O)O
• Formula: C11 H19 N O8
• Name: prop-2-en-1-yl 7-O-carbamoyl-L-glycero-alpha-D-manno-heptopyranoside;
  prop-2-en-1-yl 7-O-carbamoyl-L-glycero-alpha-D-manno-heptoside;
  prop-2-en-1-yl 7-O-carbamoyl-L-glycero-D-manno-heptoside;
  prop-2-en-1-yl 7-O-carbamoyl-L-glycero-manno-heptoside
• ZINC: ZINC000016052533
• PDB chain: 2rid Chain C Residue 503

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2rid Recognition of heptoses and the inner core of bacterial lipopolysaccharides by surfactant protein d.
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): E321 N323 D325 E329 N341 R343
• Binding residue (residue number reindexed from 1): E115 N117 D119 E123 N135 R137
• Annotation score: 1
• Binding affinity: MOAD: ic50=1.7mM

External links

• PDB: RCSB:2rid, PDBe:2rid, PDBj:2rid
• PDBsum: 2rid
• PubMed: 18092821
• UniProt: P35247|SFTPD_HUMAN Pulmonary surfactant-associated protein D (Gene Name=SFTPD)