Structure of PDB 2rib Chain A Binding Site BS04

Receptor Information

>2rib Chain A (length=150) Species: 9606 (Homo sapiens)

SLRQQVEALQGQVQHLQAAFSQYKKVELFPNGQSVGEKIFKTAGFVKPFT
EAQLLCTQAGGQLASPRSAAENAALQQLVVAKNEAAFLSMTDSKTEGKFT
YPTGESLVYSNWAPGEPNDDGGSEDCVEIFTNGKWNDRACGEKRLVVCEF

Ligand information

• Ligand ID: GMH
• InChI: InChI=1S/C7H14O7/c8-1-2(9)6-4(11)3(10)5(12)7(13)14-6/h2-13H,1H2/t2-,3-,4-,5-,6+,7-/m0/s1
• InChIKey: BGWQRWREUZVRGI-QQABCQGCSA-N
• SMILES:
  CACTVS 3.341: OC[C@H](O)[C@H]1O[C@H](O)[C@@H](O)[C@@H](O)[C@@H]1O
  OpenEye OEToolkits 1.5.0: C(C(C1C(C(C(C(O1)O)O)O)O)O)O
  CACTVS 3.341: OC[CH](O)[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O
  ACDLabs 10.04: OC1C(O)C(OC(O)C1O)C(O)CO
  OpenEye OEToolkits 1.5.0: C([C@@H]([C@@H]1[C@H]([C@@H]([C@@H]([C@H](O1)O)O)O)O)O)O
• Formula: C7 H14 O7
• Name: L-glycero-alpha-D-manno-heptopyranose;
  L-glycero-alpha-D-manno-heptose;
  L-glycero-D-manno-heptose;
  L-glycero-manno-heptose;
  L-GLYCERO-D-MANNO-HEPTOPYRANOSE
• DrugBank: DB04526
• PDB chain: 2rib Chain A Residue 356

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2rib 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
• Binding residue (residue number reindexed from 1): E116 N118 D120 E124 N136
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=2.82,IC50=1.5mM

External links

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