Structure of PDB 5ykf Chain B Binding Site BS01

Receptor Information

>5ykf Chain B (length=1309) Species: 10036 (Mesocricetus auratus)

NGCFVDALNVVPHVFLLFITFPILFIGWGSTWLHFPGHNLRWILTFILLF
VLVCEIAEGILSDHLHLYMPAGMAFMAAITSVVYYHNIETSNFPKLLIAL
LIYWTLAFITKTIKFVKFYDHLRFCLTGLLVILYGMLLLVEVNVIRVRRY
IFFKTPREVKPPEDLQDLGVRFLQPFVNLLSKGTYWWMNAFIKTAHKKPI
DLRAIGKLPIAMRALTNYQRLCVAFDAQARKDGARAIWRALCHAFGRRLI
LSSTFRILADLLGFAGPLCIFGIVDHLGKNAYVLAVLLFLALLLQRTFLQ
ASYYVAIETGINLRGAIQTKIYNKIMHLSTSNEMTAGQICNLVAIDTNQL
MWFFFLCPNLWAMPVQIIVGVILLYYILGVSALIGAAVIILLAPVQYFVA
TKLSQAQRSTLEHSNERLKQTNEMLRGMKLLKLYAWESIFCSRVEVTRRK
EMTSLRAFAVYTSISIFMNTAIPIAAVLITFVGHVSFFKESDLSPSVAFA
SLSLFHILVTPLFLLSSVVRSTVKALVSVQKLSEFLSSCVQIIGGFFTWT
PDGIPTLSNITIRIPRGQLTMIVGQVGCGKSSLLLATLGEMQKVSGAVFW
GPVAYASQKPWLLNATVEENITFESPFNKQRYKMVIEACSLQPDIDILPH
GDQTQIGERGINLSGGQRQRISVARALYQQTNVVFLDDPFSALDVHLSDH
LMQAGILELLRDDKRTVVLVTHKLQYLPHADWIIAMKDGTIQREGTLKDF
QRSEIPWRACTKYLSSAGILLLSLLVFSQLLKHMVLVAIDYWLAKWTDSD
QSVYAMVFTLLCSLGIVLCLVTSVTVEWTGLKVAKRLHRSLLNRIILAPM
RFFETTPLGSILNRFSSDCNTIDQHIPSTLECLSRSTLLCVSALTVISYV
TPVFLVALLPLAVVCYFIQKYFRVASRDLQQLDDTTQLPLLSHFAETVEG
LTTIRAFRYEARFQQKLLEYTDSNNIASLFLTAANRWLEVRMEYIGACVV
LIAAATSISNSLHRELSAGLVGLGLTYALMVSNYLNWMVRNLADMEIQLG
AVKRIHALLKTPSLIPKNWPDQGKIQIQNLSVRYDSSLKPVLKHVNALIS
PGQKIGICGRTGSGKSSFSLAFFRMVDMFEGRIIIDGIDIAKLPLHTLRS
RLSIILQDPVLFSGTIRFNLDPEKKCSDSTLWEALEIAQLKLVVKALPGG
LDAIITEGGENFSQGQRQLFCLARAFVRKTSIFIMDEATASIDMATENIL
QKVVMTAFADRTVVTIAHRVHTILSADLVMVLKRGAILEFDKPETLLSQK
DSVFASFVR

Ligand information

• Ligand ID: GBM
• InChI: InChI=1S/C23H28ClN3O5S/c1-32-21-12-9-17(24)15-20(21)22(28)25-14-13-16-7-10-19(11-8-16)33(30,31)27-23(29)26-18-5-3-2-4-6-18/h7-12,15,18H,2-6,13-14H2,1H3,(H,25,28)(H2,26,27,29)
• InChIKey: ZNNLBTZKUZBEKO-UHFFFAOYSA-N
• SMILES:
  ACDLabs 12.01: O=C(NC1CCCCC1)NS(=O)(=O)c3ccc(CCNC(=O)c2c(OC)ccc(Cl)c2)cc3
  CACTVS 3.385: COc1ccc(Cl)cc1C(=O)NCCc2ccc(cc2)[S](=O)(=O)NC(=O)NC3CCCCC3
  OpenEye OEToolkits 1.9.2: COc1ccc(cc1C(=O)NCCc2ccc(cc2)S(=O)(=O)NC(=O)NC3CCCCC3)Cl
• Formula: C23 H28 Cl N3 O5 S
• Name: 5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide;
  Glibenclamide;
  Glyburide
• ChEMBL: CHEMBL472
• DrugBank: DB01016
• ZINC: ZINC000000537805
• PDB chain: 5ykf Chain B Residue 2001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ykf Ligand binding and conformational changes of SUR1 subunit in pancreatic ATP-sensitive potassium channels.
• Resolution: 4.33 Å
• Binding residue (original residue number in PDB): R306 Y377 I381 F433 L434 N437 L592 T1242 R1246
• Binding residue (residue number reindexed from 1): R256 Y303 I307 F355 L356 N359 L514 T982 R986
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0005267 potassium channel activity
• GO:0005524 ATP binding
• GO:0008281 sulfonylurea receptor activity
• GO:0016887 ATP hydrolysis activity
• GO:0019829 ATPase-coupled monoatomic cation transmembrane transporter activity
• GO:0042626 ATPase-coupled transmembrane transporter activity
• GO:0043531 ADP binding
• GO:0044325 transmembrane transporter binding
• GO:0140359 ABC-type transporter activity

Biological Process

• GO:0001508 action potential
• GO:0006813 potassium ion transport
• GO:0031669 cellular response to nutrient levels
• GO:0035774 positive regulation of insulin secretion involved in cellular response to glucose stimulus
• GO:0046676 negative regulation of insulin secretion
• GO:0050905 neuromuscular process
• GO:0055085 transmembrane transport
• GO:0061535 glutamate secretion, neurotransmission
• GO:0071805 potassium ion transmembrane transport
• GO:0098655 monoatomic cation transmembrane transport
• GO:0098662 inorganic cation transmembrane transport

Cellular Component

• GO:0005886 plasma membrane
• GO:0008282 inward rectifying potassium channel
• GO:0016020 membrane
• GO:0032991 protein-containing complex
• GO:0098793 presynapse

External links

• PDB: RCSB:5ykf, PDBe:5ykf, PDBj:5ykf
• PDBsum: 5ykf
• PubMed: 29594720
• UniProt: A0A1U7R319