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- ChemComp-YSV: (1R,3R)-5-(2-((1R,3aS,7aR,E)-1-((R)-6-hydroxy-6-methylheptan-2-yl... -

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Open data


ID or keywords:

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Basic information

EntryDatabase: PDB chemical components / ID: YSV
NameName: (1R,3R)-5-(2-((1R,3aS,7aR,E)-1-((R)-6-hydroxy-6-methylheptan-2-yl)-7a-methyloctahydro-4H-inden-4-ylidene)ethylidene)-2-
Synonyms: 2-methylidene-19-nor-1alpha,25-dihydroxyvitamin D3

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Chemical information

Composition
Formula: C27H44O3 / Number of atoms: 74 / Formula weight: 416.636 / Formal charge: 0
Others

5b41

Type: NON-POLYMER / PDB classification: HETAIN / Three letter code: YSV / Ideal coordinates details: Corina / Model coordinates PDB-ID: 5B41
History
Create componentMar 30, 2016
Modify model coordinates codeJun 7, 2016
Initial releaseDec 7, 2016
Modify synonymsJun 5, 2020
External linksUniChem / ChemSpider / BindingDB / ChEMBL / LipidMaps / Nikkaji / PubChem / PubChem_TPharma / ZINC / Wikipedia search / Google search

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Details

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SMILES

ACDLabs 12.01OC(C)(C)CCCC(C)C1CCC2C1(CCCC2=[C@H][C@H]=C3CC(C(\C(C3)O)=C)O)C
CACTVS 3.385C[CH](CCCC(C)(C)O)[CH]1CC[CH]2C(CCC[C]12C)=CC=C3C[CH](O)C(=C)[CH](O)C3
OpenEye OEToolkits 2.0.4CC(CCCC(C)(C)O)C1CCC2C1(CCCC2=CC=C3CC(C(=C)C(C3)O)O)C

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SMILES CANONICAL

CACTVS 3.385C[C@H](CCCC(C)(C)O)[C@H]1CC[C@H]2/C(CCC[C@]12C)=C/C=C/3C[C@@H](O)C(=C)[C@H](O)C/3
OpenEye OEToolkits 2.0.4C[C@H](CCCC(C)(C)O)[C@H]1CC[C@@H]\2[C@@]1(CCC/C2=C\C=C3C[C@H](C(=C)[C@@H](C3)O)O)C

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InChI

InChI 1.03InChI=1S/C27H44O3/c1-18(8-6-14-26(3,4)30)22-12-13-23-21(9-7-15-27(22,23)5)11-10-20-16-24(28)19(2)25(29)17-20/h10-11,18,22-25,28-30H,2,6-9,12-17H2,1,3-5H3/b21-11+/t18-,22-,23+,24-,25-,27-/m1/s1

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InChIKey

InChI 1.03UHMPCVGLSKFXHR-JUTHDLPNSA-N

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SYSTEMATIC NAME

ACDLabs 12.01(1R,3R,7E,17beta)-17-[(2R)-6-hydroxy-6-methylheptan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol
OpenEye OEToolkits 2.0.4(1~{R},3~{R})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-7~{a}-methyl-1-[(2~{R})-6-methyl-6-oxidanyl-heptan-2-yl]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol

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PDB entries

Showing all 2 items

PDB-5b41:
Crystal structure of VDR-LBD complexed with 2-methylidene-19-nor-1a,25-dihydroxyvitamin D3

PDB-6jez:
Covalent labeling of rVDR-LBD by turn-on fluorescent probe mediated by conjugate addition and cyclization

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