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- ChemComp-57M: Muraymycin D2 -

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Basic information

EntryDatabase: PDB chemical components / ID: 57M
NameName: Muraymycin D2
Synonyms: N-({(1S)-2-{[(2S)-1-{[3-({(1S,2S)-2-[(5-amino-5-deoxy-beta-D-ribofuranosyl)oxy]-1-carboxy-2-[(2S,3S,4R,5R)-5-(2,4-dioxo

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Chemical information

Composition
Formula: C37H61N11O16 / Number of atoms: 125 / Formula weight: 915.944 / Formal charge: 0
Others

5ckr

Type: NON-POLYMER / PDB classification: HETAD / Three letter code: 57M / Ideal coordinates details: Corina / Model coordinates PDB-ID: 5CKR
History
Create componentAug 7, 2015
Initial releaseMar 2, 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

ACDLabs 12.01C(CNC(C(CC(C)C)NC(=O)C(C1NC(N)=NCC1)NC(=O)NC(C(C)C)C(=O)O)=O)CNC(C(OC2C(O)C(C(O2)CN)O)C3C(O)C(C(O3)N4C=CC(NC4=O)=O)O)C(O)=O
CACTVS 3.385CC(C)C[CH](NC(=O)[CH](NC(=O)N[CH](C(C)C)C(O)=O)[CH]1CCN=C(N)N1)C(=O)NCCCN[CH]([CH](O[CH]2O[CH](CN)[CH](O)[CH]2O)[CH]3O[CH]([CH](O)[CH]3O)N4C=CC(=O)NC4=O)C(O)=O
OpenEye OEToolkits 1.9.2CC(C)CC(C(=O)NCCCNC(C(C1C(C(C(O1)N2C=CC(=O)NC2=O)O)O)OC3C(C(C(O3)CN)O)O)C(=O)O)NC(=O)C(C4CCN=C(N4)N)NC(=O)NC(C(C)C)C(=O)O

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SMILES CANONICAL

CACTVS 3.385CC(C)C[C@H](NC(=O)[C@@H](NC(=O)N[C@@H](C(C)C)C(O)=O)[C@@H]1CCN=C(N)N1)C(=O)NCCCN[C@@H]([C@H](O[C@@H]2O[C@H](CN)[C@@H](O)[C@H]2O)[C@H]3O[C@H]([C@H](O)[C@@H]3O)N4C=CC(=O)NC4=O)C(O)=O
OpenEye OEToolkits 1.9.2CC(C)C[C@@H](C(=O)NCCCN[C@@H]([C@@H]([C@@H]1[C@H]([C@H]([C@@H](O1)N2C=CC(=O)NC2=O)O)O)O[C@H]3[C@@H]([C@@H]([C@H](O3)CN)O)O)C(=O)O)NC(=O)[C@H]([C@@H]4CCN=C(N4)N)NC(=O)N[C@@H](C(C)C)C(=O)O

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InChI

InChI 1.03InChI=1S/C37H61N11O16/c1-14(2)12-17(43-30(55)21(16-6-10-42-35(39)44-16)47-36(60)46-20(15(3)4)32(56)57)29(54)41-9-5-8-40-22(33(58)59)27(64-34-26(53)23(50)18(13-38)62-34)28-24(51)25(52)31(63-28)48-11-7-19(49)45-37(48)61/h7,11,14-18,20-28,31,34,40,50-53H,5-6,8-10,12-13,38H2,1-4H3,(H,41,54)(H,43,55)(H,56,57)(H,58,59)(H3,39,42,44)(H,45,49,61)(H2,46,47,60)/t16-,17-,18+,20-,21-,22-,23+,24-,25+,26+,27-,28-,31+,34-/m0/s1

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InChIKey

InChI 1.03RRTIONDZEJYWBN-VDXVSALRSA-N

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SYSTEMATIC NAME

ACDLabs 12.01N-({(1S)-2-{[(2S)-1-{[3-({(1S,2S)-2-[(5-amino-5-deoxy-beta-D-ribofuranosyl)oxy]-1-carboxy-2-[(2S,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]ethyl}amino)propyl]amino}-4-methyl-1-oxopentan-2-yl]amino}-1-[(4S)-2-amino-3,4,5,6-tetrahydropyrimidin-4-yl]-2-oxoethyl}carbamoyl)-L-valine
OpenEye OEToolkits 1.9.2(2S)-2-[[(1S)-2-[[(2S)-1-[3-[[(1S,2S)-1-[(2S,3R,4S,5R)-5-(aminomethyl)-3,4-bis(oxidanyl)oxolan-2-yl]oxy-1-[(2S,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]-3-oxidanyl-3-oxidanylidene-propan-2-yl]amino]propylamino]-4-methyl-1-oxidanylidene-pentan-2-yl]amino]-1-[(6S)-2-azanyl-1,4,5,6-tetrahydropyrimidin-6-yl]-2-oxidanylidene-ethyl]carbamoylamino]-3-methyl-butanoic acid

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PDB entries

Showing all 1 items

PDB-5ckr:
Crystal Structure of MraY in complex with Muraymycin D2

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