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- ChemComp-TOI: (1~{R},2~{S},5~{S},6~{S})-2-[(1~{S})-1-[3-[(4-azanylidene-2-methy... -

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Basic information

EntryDatabase: PDB chemical components / ID: TOI
NameName: (1~{R},2~{S},5~{S},6~{S})-2-[(1~{S})-1-[3-[(4-azanylidene-2-methyl-1~{H}-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl
Synonyms: ThDP, decarboxylated 2-oxoglutarate and isochorismate adduct, covalent intermediate II

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Chemical information

Composition
Formula: C26H35N4O16P2S / Number of atoms: 84 / Formula weight: 753.586 / Formal charge: 1
Others

5esu

Type: NON-POLYMER / PDB classification: HETAIN / Three letter code: TOI / Ideal coordinates details: Corina / Model coordinates PDB-ID: 5ESU
History
Create componentNov 17, 2015
Initial releaseJun 22, 2016
Modify synonymsJun 5, 2020
External linksUniChem / ChemSpider / Wikipedia search / Google search

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Details

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SMILES

CACTVS 3.385CC1=NC(=N)C(=CN1)C[n+]2c(C)c(CCO[P](O)(=O)O[P](O)(O)=O)sc2[C](O)(CCC(O)=O)[CH]3C=C[CH](OC(=C)C(O)=O)[CH](O)[CH]3C(O)=O
OpenEye OEToolkits 2.0.4Cc1c(sc([n+]1CC2=CNC(=NC2=N)C)C(CCC(=O)O)(C3C=CC(C(C3C(=O)O)O)OC(=C)C(=O)O)O)CCOP(=O)(O)OP(=O)(O)O

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SMILES CANONICAL

CACTVS 3.385CC1=NC(=N)C(=CN1)C[n+]2c(C)c(CCO[P](O)(=O)O[P](O)(O)=O)sc2[C@](O)(CCC(O)=O)[C@H]3C=C[C@H](OC(=C)C(O)=O)[C@@H](O)[C@@H]3C(O)=O
OpenEye OEToolkits 2.0.4[H]/N=C/1\C(=CNC(=N1)C)C[n+]2c(c(sc2[C@](CCC(=O)O)([C@H]3C=C[C@@H]([C@H]([C@@H]3C(=O)O)O)OC(=C)C(=O)O)O)CCOP(=O)(O)OP(=O)(O)O)C

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InChI

InChI 1.03InChI=1S/C26H34N4O16P2S/c1-12-18(7-9-44-48(42,43)46-47(39,40)41)49-25(30(12)11-15-10-28-14(3)29-22(15)27)26(38,8-6-19(31)32)16-4-5-17(45-13(2)23(34)35)21(33)20(16)24(36)37/h4-5,10,16-17,20-21,33,38H,2,6-9,11H2,1,3H3,(H7-,27,28,29,31,32,34,35,36,37,39,40,41,42,43)/p+1/t16-,17-,20+,21+,26-/m0/s1

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InChIKey

InChI 1.03AJVZCJMDQDMTBE-BLORIJLWSA-O

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PDB entries

Showing all 2 items

PDB-5esu:
Crystal Structure of M. tuberculosis MenD bound to Mg2+ and Covalent Intermediate II (a ThDP + de-carboxylated 2-oxoglutarate + Isochorismate adduct)

PDB-6o04:
M.tb MenD IntII bound with Inhibitor

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