Structure of PDB 5bvb Chain B Binding Site BS01

Receptor Information

>5bvb Chain B (length=126) Species: 32630 (synthetic construct)

SMNAKEILVHSLRLLENGDARGWCDLFHPEGVLEYPYAPPGWKTRFEGRE
TIWAHMRLHPEHVTWRFTDVQFYETADPDLAIGEYHGDGVVTVSGGKYAA
DYITVLRTRDGQILLLRVFWNPLRIL

Ligand information

• Ligand ID: DOG
• InChI: InChI=1S/C23H34O5/c1-21-7-5-15(24)10-14(21)3-4-17-18(21)11-19(25)22(2)16(6-8-23(17,22)27)13-9-20(26)28-12-13/h9,14-19,24-25,27H,3-8,10-12H2,1-2H3/t14-,15+,16-,17-,18+,19-,21+,22+,23+/m1/s1
• InChIKey: SHIBSTMRCDJXLN-KCZCNTNESA-N
• SMILES:
  CACTVS 3.341: C[C@]12CC[C@H](O)C[C@H]1CC[C@@H]3[C@@H]2C[C@@H](O)[C@]4(C)[C@H](CC[C@]34O)C5=CC(=O)OC5
  CACTVS 3.341: C[C]12CC[CH](O)C[CH]1CC[CH]3[CH]2C[CH](O)[C]4(C)[CH](CC[C]34O)C5=CC(=O)OC5
  ACDLabs 10.04: O=C1OCC(=C1)C5C4(C(O)CC3C(CCC2CC(O)CCC23C)C4(O)CC5)C
  OpenEye OEToolkits 1.5.0: CC12CCC(CC1CCC3C2CC(C4(C3(CCC4C5=CC(=O)OC5)O)C)O)O
  OpenEye OEToolkits 1.5.0: C[C@]12CC[C@@H](C[C@H]1CC[C@@H]3[C@@H]2C[C@H]([C@]4([C@@]3(CC[C@@H]4C5=CC(=O)OC5)O)C)O)O
• Formula: C23 H34 O5
• Name: DIGOXIGENIN;
  4-(3,12,14-TRIHYDROXY-10,13-DIMETHYL-HEXADECAHYDRO-CYCLOPENTA[A]PHENANTHREN-17-YL)-5H-FURAN-2-ONE
• ChEMBL: CHEMBL1153
• DrugBank: DB03671
• ZINC: ZINC000003982471
• PDB chain: 5bvb Chain B Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5bvb CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge.
• Resolution: 2.06 Å
• Binding residue (original residue number in PDB): L14 Y34 M55 W64 Y84 Y101
• Binding residue (residue number reindexed from 1): L15 Y35 M56 W65 Y85 Y102
• Annotation score: 1
• Binding affinity: MOAD: Kd=0.498uM

External links

• PDB: RCSB:5bvb, PDBe:5bvb, PDBj:5bvb
• PDBsum: 5bvb
• PubMed: 26419257