Structure of PDB 3bpc Chain B Binding Site BS01

Receptor Information

>3bpc Chain B (length=214) Species: 10090 (Mus musculus)

EVKLVESGGGLVQSGGSLRLSCATSGFTFTDYYMSWVRQPPGKALEWLGF
IRNKANGYTTEYSPSVKGRFTISRDNSQSILYLQMNTLRAEDSATYYCAR
DHDGYYERFSYWGQGTLVTVSAAKTTPPSVYPLAPSMVTLGCLVKGYFPE
PVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVA
HPASSTKVDKKIVP

Ligand information

• Ligand ID: KDA
• InChI: InChI=1S/C11H18O8/c1-2-3-18-11(10(16)17)4-6(13)8(15)9(19-11)7(14)5-12/h2,6-9,12-15H,1,3-5H2,(H,16,17)/t6-,7-,8-,9-,11-/m1/s1
• InChIKey: LEEKAQBTVJRLOA-UEWQFTGXSA-N
• SMILES:
  CACTVS 3.341: OC[C@@H](O)[C@H]1O[C@@](C[C@@H](O)[C@H]1O)(OCC=C)C(O)=O
  ACDLabs 10.04: O=C(O)C1(OC\C=C)OC(C(O)CO)C(O)C(O)C1
  OpenEye OEToolkits 1.5.0: C=CCOC1(CC(C(C(O1)C(CO)O)O)O)C(=O)O
  OpenEye OEToolkits 1.5.0: C=CCO[C@@]1(C[C@H]([C@H]([C@H](O1)[C@@H](CO)O)O)O)C(=O)O
  CACTVS 3.341: OC[CH](O)[CH]1O[C](C[CH](O)[CH]1O)(OCC=C)C(O)=O
• Formula: C11 H18 O8
• Name: prop-2-en-1-yl 3-deoxy-alpha-D-manno-oct-2-ulopyranosidonic acid;
  (3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID)-2-O-ALLYL;
  prop-2-en-1-yl 3-deoxy-alpha-D-manno-oct-2-ulosidonic acid;
  prop-2-en-1-yl 3-deoxy-D-manno-oct-2-ulosidonic acid;
  prop-2-en-1-yl 3-deoxy-manno-oct-2-ulosidonic acid
• ZINC: ZINC000005852687
• PDB chain: 3bpc Chain C Residue 1

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3bpc Exploration of specificity in germline monoclonal antibody recognition of a range of natural and synthetic epitopes.
• Resolution: 1.85 Å
• Binding residue (original residue number in PDB): Y33 R52 N52D E100A
• Binding residue (residue number reindexed from 1): Y33 R52 N56 E107
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=4.80,Kd=16uM

External links

• PDB: RCSB:3bpc, PDBe:3bpc, PDBj:3bpc
• PDBsum: 3bpc
• PubMed: 18272175