Structure of PDB 2by4 Chain A Binding Site BS01

Receptor Information
>2by4 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 IDAD4
InChIInChI=1S/C47H75NO14/c1-11-13-14-20-23-27-35(51)58-39-37-36(31(4)38(39)59-41(52)30(3)12-2)40-47(56,46(10,55)42(53)60-40)33(29-45(37,9)61-32(5)49)57-34(50)26-24-21-18-16-15-17-19-22-25-28-48-43(54)62-44(6,7)8/h12,33,37-40,55-56H,11,13-29H2,1-10H3,(H,48,54)/b30-12-/t33-,37+,38-,39-,40-,45-,46+,47+/m0/s1
InChIKeyIBTNJSDBPZIGKM-GGGDSPQJSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CCCCCCCC(=O)O[CH]1[CH](OC(=O)C(C)=CC)C(=C2[CH]3OC(=O)[C](C)(O)[C]3(O)[CH](C[C](C)(OC(C)=O)[CH]12)OC(=O)CCCCCCCCCCCNC(=O)OC(C)(C)C)C
CACTVS 3.341CCCCCCCC(=O)O[C@@H]1[C@@H](OC(=O)\C(C)=C/C)C(=C2[C@@H]3OC(=O)[C@@](C)(O)[C@@]3(O)[C@H](C[C@](C)(OC(C)=O)[C@@H]12)OC(=O)CCCCCCCCCCCNC(=O)OC(C)(C)C)C
OpenEye OEToolkits 1.5.0CCCCCCCC(=O)OC1C2C(=C(C1OC(=O)C(=CC)C)C)C3C(C(CC2(C)OC(=O)C)OC(=O)CCCCCCCCCCCNC(=O)OC(C)(C)C)(C(C(=O)O3)(C)O)O
OpenEye OEToolkits 1.5.0CCCCCCCC(=O)O[C@H]1[C@H]2C(=C([C@@H]1OC(=O)/C(=C\C)/C)C)[C@H]3[C@]([C@H](C[C@]2(C)OC(=O)C)OC(=O)CCCCCCCCCCCNC(=O)OC(C)(C)C)([C@](C(=O)O3)(C)O)O
ACDLabs 10.04O=C(OC(C)(C)C)NCCCCCCCCCCCC(=O)OC2CC(OC(=O)C)(C1C(=C(C(OC(=O)\C(=C/C)C)C1OC(=O)CCCCCCC)C)C3OC(=O)C(O)(C)C23O)C
FormulaC47 H75 N O14
Name(3S,3AR,4S,6S,6AR,7S,8S,9BS)-6-(ACETYLOXY)-3,3A-DIHYDROXY-3,6,9-TRIMETHYL-8-{[(2Z)-2-METHYLBUT-2-ENOYL]OXY}-7-(OCTANOYLOXY)-2-OXO-2,3,3A,4,5,6,6A,7,8,9B-DECAHYDROAZULENO[4,5-B]FURAN-4-YL 12-[(TERT-BUTOXYCARBONYL)AMINO]DODECANOATE;
((((3'-DEOXY-3'-THYMIDINYL)-AMINO)CARBONYL)METHYL)
ChEMBL
DrugBank
ZINCZINC000150341956
PDB chain2by4 Chain A Residue 1995 [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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PDB2by4 Natural Products as Starting Materials for Development of Second-Generation Serca Inhibitors Targeted Towards Prostate Cancer Cells
Resolution3.3 Å
Binding residue
(original residue number in PDB)		L61 V62 N101 L253 E255 F256 Q259 L260 V263 I307 L311 P312 V769 V772 L828 I829 F834
Binding residue
(residue number reindexed from 1)		L61 V62 N101 L253 E255 F256 Q259 L260 V263 I307 L311 P312 V769 V772 L828 I829 F834
Annotation score1
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2by4, PDBe:2by4, PDBj:2by4
PDBsum2by4
PubMed16412648
UniProtP04191|AT2A1_RABIT Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 (Gene Name=ATP2A1)

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