Structure of PDB 3ijh Chain B Binding Site BS01

Receptor Information

>3ijh Chain B (length=221) Species: 10090 (Mus musculus)

EVMLVESGGGLVQPGNSLRLSCATSGFTFTDYYMSWVRQPPGKALEWLGF
IRNKAKGYTTEYSASVKGRFTISRDNSQSILYLQMNTLRAEDSATYYCAR
DISPSYGVYYEGFAYWGQGTLVTVSAATTTAPSVYPLVPGGSSVTLGCLV
KGYFPEPVTVKWNYGALSSGVRTVSSVLQSGFYSLSSLVTVPSSTWPSQT
VICNVAHPASKTELIKRIEPR

Ligand information

• Ligand ID: KO2
• InChI: InChI=1S/C11H18O9/c1-2-3-19-11(10(17)18)9(16)7(15)6(14)8(20-11)5(13)4-12/h2,5-9,12-16H,1,3-4H2,(H,17,18)/t5-,6-,7+,8-,9+,11-/m1/s1
• InChIKey: MJWRJGHIYDIAQR-RUEXUQCSSA-N
• SMILES:
  CACTVS 3.341: OC[CH](O)[CH]1O[C](OCC=C)([CH](O)[CH](O)[CH]1O)C(O)=O
  CACTVS 3.341: OC[C@@H](O)[C@H]1O[C@](OCC=C)([C@@H](O)[C@@H](O)[C@H]1O)C(O)=O
  OpenEye OEToolkits 1.5.0: C=CCO[C@@]1([C@H]([C@H]([C@H]([C@H](O1)[C@@H](CO)O)O)O)O)C(=O)O
  OpenEye OEToolkits 1.5.0: C=CCOC1(C(C(C(C(O1)C(CO)O)O)O)O)C(=O)O
  ACDLabs 10.04: O=C(O)C1(OC\C=C)OC(C(O)CO)C(O)C(O)C1O
• Formula: C11 H18 O9
• Name: prop-2-en-1-yl D-glycero-alpha-D-talo-oct-2-ulopyranosidonic acid;
  prop-2-en-1-yl D-glycero-alpha-D-talo-oct-2-ulosidonic acid;
  prop-2-en-1-yl D-glycero-D-talo-oct-2-ulosidonic acid;
  prop-2-en-1-yl D-glycero-talo-oct-2-ulosidonic acid
• ZINC: ZINC000058638803
• PDB chain: 3ijh Chain B Residue 214

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3ijh The role of CDR H3 in antibody recognition of a synthetic analog of a lipopolysaccharide antigen.
• Resolution: 2.1 Å
• Binding residue (original residue number in PDB): Y33 R52 K53 I96 P98 E100E
• Binding residue (residue number reindexed from 1): Y33 R52 K56 I102 P104 E111
• Annotation score: 1
• Binding affinity: MOAD: Kd=100uM
  PDBbind-CN: -logKd/Ki=4.00,Kd=100uM

External links

• PDB: RCSB:3ijh, PDBe:3ijh, PDBj:3ijh
• PDBsum: 3ijh
• PubMed: 19767317