Structure of PDB 4ycm Chain A Binding Site BS01

Receptor Information
>4ycm Chain A (length=994) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MEAAHSKSTEECLAYFGVSETTGLTPDQVKRHLEKYGHNELPAEEGKSLW
ELVIEQFEDLLVRILLLAACISFVLAWFEEGEETITAFVEPFVILLILIA
NAIVGVWQERNAENAIEALKEYEPEMGKVYRADRKSVQRIKARDIVPGDI
VEVAVGDKVPADIRILSIKSTTLRVDQSILTGESVSVIKHTEPVPDPRAV
NQDKKNMLFSGTNIAAGKALGIVATTGVSTEIGKIRDQMAATEQDKTPLQ
QKLDEFGEQLSKVISLICVAVWLINIGHFNDPVHGGSWIRGAIYYFKIAV
ALAVAAIPEGLPAVITTCLALGTRRMAKKNAIVRSLPSVETLGCTSVICS
DKTGTLTTNQMSVCKMFIIDKVDGDFCSLNEFSITGSTYAPEGEVLKNDK
PIRSGQFDGLVELATICALCNDSSLDFNETKGVYEKVGEATETALTTLVE
KMNVFNTEVRNLSKVERANACNSVIRQLMKKEFTLEFSRDRKSMSVYCSP
AKSSRAAVGNKMFVKGAPEGVIDRCNYVRVGTTRVPMTGPVKEKILSVIK
EWGTGRDTLRCLALATRDTPPKREEMVLDDSSRFMEYETDLTFVGVVGML
DPPRKEVMGSIQLCRDAGIRVIMITGDNKGTAIAICRRIGIFGENEEVAD
RAYTGREFDDLPLAEQREACRRACCFARVEPSHKSKIVEYLQSYDEITAM
TGDGVNDAPALKKAEIGIAMGSGTAVAKTASEMVLADDNFSTIVAAVEEG
RAIYNNMKQFIRYLISSNVGEVVCIFLTAALGLPEALIPVQLLWVNLVTD
GLPATALGFNPPDLDIMDRPPRSPKEPLISGWLFFRYMAIGGYVGAATVG
AAAWWFMYAEDGPGVTYHQLTHFMQCTEDHPHFEGLDCEIFEAPEPMTMA
LSVLVTIEMCNALNSLSENQSLMRMPPWVNIWLLGSICLSMSLHFLILYV
DPLPMIFKLKALDLTQWLMVLKISLPVIGLDEILKFIARNYLEG
Ligand information
Ligand ID7BS
InChIInChI=1S/C34H52O9/c1-7-8-14-24(3)20-26-16-12-10-9-11-15-23(2)19-25(4)28(39-5)18-13-17-27(21-30(36)41-26)42-34-32(38)33(40-6)31(37)29(22-35)43-34/h7-13,17,19-20,23,26-29,31-35,37-38H,14-16,18,21-22H2,1-6H3/b8-7+,11-9+,12-10+,17-13+,24-20-,25-19+/t23-,26+,27+,28-,29+,31+,32+,33-,34+/m0/s1
InChIKeyQLNOFWPLTFNJPW-CMAVNLJPSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CO[CH]1CC=C[CH](CC(=O)O[CH](CC=CC=CC[CH](C)C=C1C)C=C(C)CC=CC)O[CH]2O[CH](CO)[CH](O)[CH](OC)[CH]2O
ACDLabs 12.01COC2CC=CC(OC1OC(C(C(C1O)OC)O)CO)CC(OC(CC=CC=CCC(C=C2C)C)[C@H]=C(C)C[C@H]=CC)=O
OpenEye OEToolkits 1.9.2CC=CCC(=CC1CC=CC=CCC(C=C(C(CC=CC(CC(=O)O1)OC2C(C(C(C(O2)CO)O)OC)O)OC)C)C)C
OpenEye OEToolkits 1.9.2C/C=C/C/C(=C\[C@H]1C/C=C/C=C/C[C@@H](/C=C(/[C@H](C/C=C/[C@H](CC(=O)O1)O[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)OC)O)OC)\C)C)/C
CACTVS 3.385CO[C@H]/1C/C=C/[C@H](CC(=O)O[C@H](C\C=C\C=C\C[C@H](C)\C=C/1C)/C=C(/C)C/C=C/C)O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](OC)[C@H]2O
FormulaC34 H52 O9
Name(4S,5E,8S,9E,11S,13E,15E,18R)-8-methoxy-9,11-dimethyl-18-[(1Z,4E)-2-methylhexa-1,4-dien-1-yl]-2-oxooxacyclooctadeca-5,9,13,15-tetraen-4-yl 3-O-methyl-beta-D-glucopyranoside;
Biselyngbyaside
ChEMBLCHEMBL4207081
DrugBank
ZINCZINC000255261107
PDB chain4ycm Chain A Residue 1004 [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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PDB4ycm Biselyngbyasides, cytotoxic marine macrolides, are novel and potent inhibitors of the Ca(2+) pumps with a unique mode of binding
Resolution3.2 Å
Binding residue
(original residue number in PDB)		Q56 D59 N101 G105 K246 Q250 L253 I307 P308 L311 P312 I315
Binding residue
(residue number reindexed from 1)		Q56 D59 N101 G105 K246 Q250 L253 I307 P308 L311 P312 I315
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.72,Ki=19nM
BindingDB: Ki=19nM
Enzymatic activity
Catalytic site (original residue number in PDB) D351 D703 D707
Catalytic site (residue number reindexed from 1) D351 D703 D707
Enzyme Commision number 7.2.2.10: P-type Ca(2+) transporter.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0005215 transporter activity
GO:0005388 P-type calcium transporter activity
GO:0005509 calcium ion binding
GO:0005524 ATP binding
GO:0016887 ATP hydrolysis activity
GO:0046872 metal ion binding
Biological Process
GO:0006816 calcium ion transport
GO:0006874 intracellular calcium ion homeostasis
GO:0031448 positive regulation of fast-twitch skeletal muscle fiber contraction
GO:0070588 calcium ion transmembrane transport
GO:0106134 positive regulation of cardiac muscle cell contraction
GO:1901896 positive regulation of ATPase-coupled calcium transmembrane transporter activity
GO:1902082 positive regulation of calcium ion import into sarcoplasmic reticulum
GO:1990036 calcium ion import into sarcoplasmic reticulum
Cellular Component
GO:0016020 membrane
GO:0016529 sarcoplasmic reticulum
GO:0033017 sarcoplasmic reticulum membrane

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Molecular Function
View graph for
Biological Process
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Cellular Component
External links
PDB RCSB:4ycm, PDBe:4ycm, PDBj:4ycm
PDBsum4ycm
PubMed25957767
UniProtP04191|AT2A1_RABIT Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 (Gene Name=ATP2A1)

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