Structure of PDB 6pyd Chain L Binding Site BS01

Receptor Information

>6pyd Chain L (length=208) Species: 10090 (Mus musculus)

VLMTQTPLSLPVSLGDQASISCRSSQSTYLEWYLQKPGQSPKLLIYKVSN
RFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPLTFGAGTK
LELKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNA
LQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSS
PVTKSFNR

Ligand information

• Ligand ID: P4S
• InChI: InChI=1S/C24H32O5/c1-21-8-5-15(25)12-23(21,27)10-7-17-16(21)6-9-22(2)18(11-19-24(17,22)29-19)14-3-4-20(26)28-13-14/h3-4,13,15-19,25,27H,5-12H2,1-2H3/t15-,16-,17+,18+,19+,21+,22+,23-,24+/m0/s1
• InChIKey: JMNQTHQLNRILMH-OBBGIPBRSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CC12CCC(CC1(CCC3C2CCC4(C35C(O5)CC4C6=COC(=O)C=C6)C)O)O
  CACTVS 3.385: C[C]12CC[CH](O)C[C]1(O)CC[CH]3[CH]2CC[C]4(C)[CH](C[CH]5O[C]345)C6=COC(=O)C=C6
  CACTVS 3.385: C[C@]12CC[C@H](O)C[C@@]1(O)CC[C@@H]3[C@@H]2CC[C@]4(C)[C@H](C[C@H]5O[C@@]345)C6=COC(=O)C=C6
  OpenEye OEToolkits 2.0.7: C[C@]12CC[C@@H](C[C@]1(CC[C@@H]3[C@@H]2CC[C@]4([C@]35[C@H](O5)C[C@@H]4C6=COC(=O)C=C6)C)O)O
  ACDLabs 12.01: C12(C)CCC(CC1(O)CCC6C2CCC4(C(C3=COC(=O)C=C3)CC5C46O5)C)O
• Formula: C24 H32 O5
• Name: (3beta,5beta,14alpha,15beta)-3,5-dihydroxy-14,15-epoxybufa-20,22-dienolide
• ZINC: ZINC000005350761
• PDB chain: 6pyd Chain H Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6pyd Kappa-on-Heavy (KoH) bodies are a distinct class of fully-human antibody-like therapeutic agents with antigen-binding properties.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): Y36 E38 G95
• Binding residue (residue number reindexed from 1): Y29 E31 G88
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=6.81,Kd=156nM

External links

• PDB: RCSB:6pyd, PDBe:6pyd, PDBj:6pyd
• PDBsum: 6pyd
• PubMed: 31879340