Structure of PDB 8py3 Chain A Binding Site BS02

Receptor Information

>8py3 Chain A (length=295) Species: 9606 (Homo sapiens)

ERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYD
NLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLL
KDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYP
LSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVD
LLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSDPFLGGGGMDFD
SKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQ

Ligand information

• Ligand ID: I1R
• InChI: InChI=1S/C29H28ClFN4O2/c1-19-23(5-2-6-26(19)31)18-35-15-3-4-20(17-35)16-27-33-28(34-37-27)21-9-13-25(14-10-21)32-29(36)22-7-11-24(30)12-8-22/h2,5-14,20H,3-4,15-18H2,1H3,(H,32,36)/t20-/m0/s1
• InChIKey: USLQGCUXEGLWGH-FQEVSTJZSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: Cc1c(cccc1F)CN2CCCC(C2)Cc3nc(no3)c4ccc(cc4)NC(=O)c5ccc(cc5)Cl
  CACTVS 3.385: Cc1c(F)cccc1CN2CCC[C@H](C2)Cc3onc(n3)c4ccc(NC(=O)c5ccc(Cl)cc5)cc4
  OpenEye OEToolkits 2.0.7: Cc1c(cccc1F)CN2CCC[C@H](C2)Cc3nc(no3)c4ccc(cc4)NC(=O)c5ccc(cc5)Cl
  CACTVS 3.385: Cc1c(F)cccc1CN2CCC[CH](C2)Cc3onc(n3)c4ccc(NC(=O)c5ccc(Cl)cc5)cc4
• Formula: C29 H28 Cl F N4 O2
• Name: 4-chloranyl-~{N}-[4-[5-[[(3~{S})-1-[(3-fluoranyl-2-methyl-phenyl)methyl]piperidin-3-yl]methyl]-1,2,4-oxadiazol-3-yl]phenyl]benzamide
• PDB chain: 8py3 Chain A Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8py3 Structure-Activity Studies of 1,2,4-Oxadiazoles for the Inhibition of the NAD + -Dependent Lysine Deacylase Sirtuin 2.
• Resolution: 1.65 Å
• Binding residue (original residue number in PDB): F96 L103 F119 L138 Y139 P140 D170 F190 V233 F234 F235 E237
• Binding residue (residue number reindexed from 1): F41 L48 F64 L83 Y84 P85 D115 F135 V178 F179 F180 E182
• Annotation score: 1

External links

• PDB: RCSB:8py3, PDBe:8py3, PDBj:8py3
• PDBsum: 8py3
• PubMed: 38847803
• UniProt: Q8IXJ6|SIR2_HUMAN NAD-dependent protein deacetylase sirtuin-2 (Gene Name=SIRT2)