Structure of PDB 3ikc Chain B Binding Site BS01

Receptor Information
>3ikc Chain B (length=221) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EVMLVESGGGLVQPGNSLRLSCATSGFTFTDYYMSWVRQPPGKALEWLGF
IRNKAKGYTTEYSASVKGRFTISRDNSQSILYLQMNTLRAEDSATYYCAR
DISPSYGVYYEGFAYWGQGTLVTVSAATTTAPSVYPLVPGGSSVTLGCLV
KGYFPEPVTVKWNYGALSSGVRTVSSVLQSGFYSLSSLVTVPSSTWPSQT
VICNVAHPASKTELIKRIEPR
Ligand information
Ligand IDKME
InChIInChI=1S/C12H20O8/c1-3-4-19-12(11(16)17)5-7(14)9(15)10(20-12)8(6-13)18-2/h3-4,7-10,13-15H,5-6H2,1-2H3,(H,16,17)/b4-3+/t7-,8-,9-,10-,12-/m1/s1
InChIKeyHGSGCVUFLKROQP-PPCCDUSGSA-N
SMILES
SoftwareSMILES
CACTVS 3.352CO[CH](CO)[CH]1O[C](C[CH](O)[CH]1O)(OC=CC)C(O)=O
CACTVS 3.352CO[C@H](CO)[C@H]1O[C@@](C[C@@H](O)[C@H]1O)(O\C=C\C)C(O)=O
OpenEye OEToolkits 1.7.0CC=COC1(CC(C(C(O1)C(CO)OC)O)O)C(=O)O
OpenEye OEToolkits 1.7.0C/C=C/O[C@@]1(C[C@H]([C@H]([C@H](O1)[C@@H](CO)OC)O)O)C(=O)O
ACDLabs 11.02O=C(O)C1(O/C=C/C)OC(C(O)C(O)C1)C(OC)CO
FormulaC12 H20 O8
Name(1E)-prop-1-en-1-yl 3-deoxy-7-O-methyl-alpha-D-manno-oct-2-ulopyranosidonic acid;
(1E)-prop-1-en-1-yl 3-deoxy-7-O-methyl-alpha-D-manno-oct-2-ulosidonic acid;
(1E)-prop-1-en-1-yl 3-deoxy-7-O-methyl-D-manno-oct-2-ulosidonic acid;
(1E)-prop-1-en-1-yl 3-deoxy-7-O-methyl-manno-oct-2-ulosidonic acid
ChEMBL
DrugBank
ZINCZINC000058649418
PDB chain3ikc Chain E Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3ikc The role of CDR H3 in antibody recognition of a synthetic analog of a lipopolysaccharide antigen.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		K53 Y100C
Binding residue
(residue number reindexed from 1)		K56 Y109
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.46,Kd=0.035uM
External links