Structure of PDB 1d6v Chain H Binding Site BS01

Receptor Information

>1d6v Chain H (length=221) Species: 10090 (Mus musculus)

QVQLQQSGAELMKPGASVKISCKATGYTFSSYWIEWVKQRPGHGLEWIGE
ILPGSGSTNYNEKFKGKATFTADTSSNTAYMQLSSLTSEDSAVYYCARGH
SYYFYDGDYWGQGTSVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVK
DYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQT
YICNVNHKPSNTKVDKKVEPK

Ligand information

• Ligand ID: HOP
• InChI: InChI=1S/C23H27NO4/c25-21-15-19(16-5-2-1-3-6-16)12-13-20(21)17-8-10-18(11-9-17)23(28)24-14-4-7-22(26)27/h1-3,5-6,8-11,19-21,25H,4,7,12-15H2,(H,24,28)(H,26,27)/t19-,20+,21-/m0/s1
• InChIKey: OBWILOKKNDYPLX-HBMCJLEFSA-N
• SMILES:
  ACDLabs 10.04: O=C(O)CCCNC(=O)c1ccc(cc1)C3CCC(c2ccccc2)CC3O
  OpenEye OEToolkits 1.5.0: c1ccc(cc1)[C@H]2CC[C@@H]([C@H](C2)O)c3ccc(cc3)C(=O)NCCCC(=O)O
  CACTVS 3.341: O[C@H]1C[C@H](CC[C@@H]1c2ccc(cc2)C(=O)NCCCC(O)=O)c3ccccc3
  OpenEye OEToolkits 1.5.0: c1ccc(cc1)C2CCC(C(C2)O)c3ccc(cc3)C(=O)NCCCC(=O)O
  CACTVS 3.341: O[CH]1C[CH](CC[CH]1c2ccc(cc2)C(=O)NCCCC(O)=O)c3ccccc3
• Formula: C23 H27 N O4
• Name: (1S,2S,5S)2-(4-GLUTARIDYLBENZYL)-5-PHENYL-1-CYCLOHEXANOL;
  OXY-COPE-HAPTEN
• DrugBank: DB07909
• ZINC: ZINC000006582201
• PDB chain: 1d6v Chain H Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1d6v Conformational effects in biological catalysis: an antibody-catalyzed oxy-cope rearrangement.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): E35 G95 H96 Y100A D101 W103
• Binding residue (residue number reindexed from 1): E35 G99 H100 Y105 D108 W110
• Annotation score: 1
• Binding affinity: MOAD: Kd=670nM
  PDBbind-CN: -logKd/Ki=6.17,Kd=670nM

External links

• PDB: RCSB:1d6v, PDBe:1d6v, PDBj:1d6v
• PDBsum: 1d6v
• PubMed: 10651626
• UniProt: P01857|IGHG1_HUMAN Immunoglobulin heavy constant gamma 1 (Gene Name=IGHG1)