Structure of PDB 3ikc Chain B Binding Site BS02

Receptor Information

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

EVMLVESGGGLVQPGNSLRLSCATSGFTFTDYYMSWVRQPPGKALEWLGF
IRNKAKGYTTEYSASVKGRFTISRDNSQSILYLQMNTLRAEDSATYYCAR
DISPSYGVYYEGFAYWGQGTLVTVSAATTTAPSVYPLVPGGSSVTLGCLV
KGYFPEPVTVKWNYGALSSGVRTVSSVLQSGFYSLSSLVTVPSSTWPSQT
VICNVAHPASKTELIKRIEPR

Ligand information

• Ligand ID: KDO
• InChI: InChI=1S/C8H14O8/c9-2-4(11)6-5(12)3(10)1-8(15,16-6)7(13)14/h3-6,9-12,15H,1-2H2,(H,13,14)/t3-,4-,5-,6-,8-/m1/s1
• InChIKey: NNLZBVFSCVTSLA-HXUQBWEZSA-N
• SMILES:
  CACTVS 3.341: OC[C@@H](O)[C@H]1O[C@](O)(C[C@@H](O)[C@H]1O)C(O)=O
  OpenEye OEToolkits 1.5.0: C1[C@H]([C@H]([C@H](O[C@]1(C(=O)O)O)[C@@H](CO)O)O)O
  OpenEye OEToolkits 1.5.0: C1C(C(C(OC1(C(=O)O)O)C(CO)O)O)O
  CACTVS 3.341: OC[CH](O)[CH]1O[C](O)(C[CH](O)[CH]1O)C(O)=O
  ACDLabs 10.04: O=C(O)C1(O)OC(C(O)CO)C(O)C(O)C1
• Formula: C8 H14 O8
• Name: 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid;
  3-deoxy-d-manno-oct-2-ulopyranosonic acid;
  2-keto-3-deoxy-D-mannooctanoic acid;
  3-deoxy-alpha-D-manno-oct-2-ulosonic acid;
  3-deoxy-D-manno-oct-2-ulosonic acid;
  3-deoxy-manno-oct-2-ulosonic acid
• DrugBank: DB03548
• ZINC: ZINC000005851513
• PDB chain: 3ikc Chain E Residue 2

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3ikc The role of CDR H3 in antibody recognition of a synthetic analog of a lipopolysaccharide antigen.
• Resolution: 2.6 Å
• Binding residue (original residue number in PDB): Y33 R52 I96 E100E
• Binding residue (residue number reindexed from 1): Y33 R52 I102 E111
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=7.46,Kd=0.035uM

External links

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