Structure of PDB 4ret Chain A Binding Site BS07

Receptor Information
>4ret Chain A (length=996) Species: 9823 (Sus scrofa) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KERDMDELKKEVSMDDHKLSLDELHRKYGTDLSRGLTPARAAEILARDGP
NALTPPPTTPEWVKFCRQLFGGFSMLLWIGAILCFLAYGIQAATEEEPQN
DNLYLGVVLSAVVIITGCFSYYQEAKSSKIMESFKNMVPQQALVIRNGEK
MSINAEEVVVGDLVEVKGGDRIPADLRIISANGCKVDNSSLTGESEPQTR
SPDFTNENPLETRNIAFFSTNCVEGTARGIVVYTGDRTVMGRIATLASGL
EGGQTPIAAEIEHFIHIITGVAVFLGVSFFILSLILEYTWLEAVIFLIGI
IVANVPEGLLATVTVCLTLTAKRMARKNCLVKNLEAVETLGSTSTICSDK
TGTLTQNRMTVAHMWSDNQIHEADTTENQSGVSFDKTSATWLALSRIAGL
CNRAVFQANQENLPILKRAVAGDASESALLKCIELCCGSVKEMRERYTKI
VEIPFNSTNKYQLSIHKNPNTAEPRHLLVMKGAPERILDRCSSILIHGKE
QPLDEELKDAFQNAYLELGGLGERVLGFCHLFLPDEQFPEGFQFDTDDVN
FPLDNLCFVGLISMIDPPRAAVPDAVGKCRSAGIKVIMVTGDHPITAKAI
AKGVGIISEGNETVEDIAARLNIPVSQVNPRDAKACVVHGSDLKDMTSEQ
LDDILKYHTEIVFARTSPQQKLIIVEGCQRQGAIVAVTGDGVNDSPASKK
ADIGVAMGIAGSDVSKQAADMILLDDNFASIVTGVEEGRLIFDNLKKSIA
YTLTSNIPEITPFLIFIIANIPLPLGTVTILCIDLGTDMVPAISLAYEQA
ESDIMKRQPRNPKTDKLVNEQLISMAYGQIGMIQALGGFFTYFVILAENG
FLPIHLLGLRVNWDDRWINDVEDSYGQQWTYEQRKIVEFTCHTPFFVTIV
VVQWADLVICKTRRNSVFQQGMKNKILIFGLFEETALAAFLSYCPGMGVA
LRMYPLKPTWWFCAFPYSLLIFVYDEVRKLIIRRRPGGWVEKETYY
Ligand information
Ligand IDDGX
InChIInChI=1S/C41H64O14/c1-19-36(47)28(42)15-34(50-19)54-38-21(3)52-35(17-30(38)44)55-37-20(2)51-33(16-29(37)43)53-24-8-10-39(4)23(13-24)6-7-26-27(39)14-31(45)40(5)25(9-11-41(26,40)48)22-12-32(46)49-18-22/h12,19-21,23-31,33-38,42-45,47-48H,6-11,13-18H2,1-5H3/t19-,20-,21-,23-,24+,25-,26-,27+,28+,29+,30+,31-,33+,34+,35+,36-,37-,38-,39+,40+,41+/m1/s1
InChIKeyLTMHDMANZUZIPE-PUGKRICDSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C1OCC(=C1)C2CCC8(O)C2(C)C(O)CC7C8CCC6CC(OC5OC(C(OC4OC(C(OC3OC(C)C(O)C(O)C3)C(O)C4)C)C(O)C5)C)CCC67C
CACTVS 3.370C[CH]1O[CH](C[CH](O)[CH]1O)O[CH]2[CH](O)C[CH](O[CH]2C)O[CH]3[CH](O)C[CH](O[CH]3C)O[CH]4CC[C]5(C)[CH](CC[CH]6[CH]5C[CH](O)[C]7(C)[CH](CC[C]67O)C8=CC(=O)OC8)C4
CACTVS 3.370C[C@H]1O[C@H](C[C@H](O)[C@@H]1O)O[C@H]2[C@@H](O)C[C@@H](O[C@@H]2C)O[C@H]3[C@@H](O)C[C@@H](O[C@@H]3C)O[C@H]4CC[C@@]5(C)[C@H](CC[C@@H]6[C@@H]5C[C@@H](O)[C@]7(C)[C@H](CC[C@]67O)C8=CC(=O)OC8)C4
OpenEye OEToolkits 1.7.2CC1C(C(CC(O1)OC2C(OC(CC2O)OC3C(OC(CC3O)OC4CCC5(C(C4)CCC6C5CC(C7(C6(CCC7C8=CC(=O)OC8)O)C)O)C)C)C)O)O
OpenEye OEToolkits 1.7.2C[C@@H]1[C@H]([C@H](C[C@@H](O1)O[C@@H]2[C@H](O[C@H](C[C@@H]2O)O[C@@H]3[C@H](O[C@H](C[C@@H]3O)O[C@H]4CC[C@]5([C@@H](C4)CC[C@@H]6[C@@H]5C[C@H]([C@]7([C@@]6(CC[C@@H]7C8=CC(=O)OC8)O)C)O)C)C)C)O)O
FormulaC41 H64 O14
NameDIGOXIN
ChEMBLCHEMBL1751
DrugBankDB00390
ZINCZINC000242548690
PDB chain4ret Chain A Residue 1107 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4ret Structures and characterization of digoxin- and bufalin-bound Na+,K+-ATPase compared with the ouabain-bound complex.
Resolution4.0 Å
Binding residue
(original residue number in PDB)		D121 N122 L125 E312 G319 V322 A323 F783 L793 R880
Binding residue
(residue number reindexed from 1)		D101 N102 L105 E292 G299 V302 A303 F763 L773 R860
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.59,Kd=26nM
Enzymatic activity
Catalytic site (original residue number in PDB) D369 D710 D714
Catalytic site (residue number reindexed from 1) D349 D690 D694
Enzyme Commision number 7.2.2.13: Na(+)/K(+)-exchanging ATPase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0005215 transporter activity
GO:0005391 P-type sodium:potassium-exchanging transporter activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008556 P-type potassium transmembrane transporter activity
GO:0016887 ATP hydrolysis activity
GO:0030955 potassium ion binding
GO:0031402 sodium ion binding
GO:0046872 metal ion binding
GO:0051117 ATPase binding
Biological Process
GO:0002028 regulation of sodium ion transport
GO:0006813 potassium ion transport
GO:0006814 sodium ion transport
GO:0006883 intracellular sodium ion homeostasis
GO:0010248 establishment or maintenance of transmembrane electrochemical gradient
GO:0030007 intracellular potassium ion homeostasis
GO:0036376 sodium ion export across plasma membrane
GO:0055085 transmembrane transport
GO:0086009 membrane repolarization
GO:1902600 proton transmembrane transport
GO:1990573 potassium ion import across plasma membrane
Cellular Component
GO:0005886 plasma membrane
GO:0005890 sodium:potassium-exchanging ATPase complex
GO:0016020 membrane
GO:0016323 basolateral plasma membrane
GO:0030424 axon
GO:0042383 sarcolemma
GO:0042470 melanosome
GO:0042995 cell projection

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4ret, PDBe:4ret, PDBj:4ret
PDBsum4ret
PubMed25624492
UniProtP05024|AT1A1_PIG Sodium/potassium-transporting ATPase subunit alpha-1 (Gene Name=ATP1A1)

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