Structure of PDB 3ikc Chain A Binding Site BS01

Receptor Information
>3ikc Chain A (length=217) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVMTQSPSSLAVSAGEKVTMSCKSSQSLLNSRTRKNYLAWYQQKPGQSPK
LLIYWASTRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCKQSNNLR
TFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINV
KWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEA
THKTSTSPIVKSFNRNE
Ligand information
Ligand IDKDO
InChIInChI=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
InChIKeyNNLZBVFSCVTSLA-HXUQBWEZSA-N
SMILES
SoftwareSMILES
CACTVS 3.341OC[C@@H](O)[C@H]1O[C@](O)(C[C@@H](O)[C@H]1O)C(O)=O
OpenEye OEToolkits 1.5.0C1[C@H]([C@H]([C@H](O[C@]1(C(=O)O)O)[C@@H](CO)O)O)O
OpenEye OEToolkits 1.5.0C1C(C(C(OC1(C(=O)O)O)C(CO)O)O)O
CACTVS 3.341OC[CH](O)[CH]1O[C](O)(C[CH](O)[CH]1O)C(O)=O
ACDLabs 10.04O=C(O)C1(O)OC(C(O)CO)C(O)C(O)C1
FormulaC8 H14 O8
Name3-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
ChEMBL
DrugBankDB03548
ZINCZINC000005851513
PDB chain3ikc Chain E Residue 2 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
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)		Y32 S91 N92 R95
Binding residue
(residue number reindexed from 1)		Y37 S96 N97 R100
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.46,Kd=0.035uM
External links