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- ChemComp-52G: Zorbamycin -

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Basic information

EntryDatabase: PDB chemical components / ID: 52G
NameName: Zorbamycin
Synonyms: (2R,3S,4S,5R,6R)-2-{[(2R,3S,4S,5S,6S)-2-{[(1R,2S)-2-[({6-amino-2-[(1S)-3-amino-1-{[(2S)-2,3-diamino-3-oxopropyl]amino}-3-oxopropyl]-5-methylpyrimidin-4-yl}carbonyl)amino]-3-{[(3R,4S,5S)-6- ...Synonyms: (2R,3S,4S,5R,6R)-2-{[(2R,3S,4S,5S,6S)-2-{[(1R,2S)-2-[({6-amino-2-[(1S)-3-amino-1-{[(2S)-2,3-diamino-3-oxopropyl]amino}-3-oxopropyl]-5-methylpyrimidin-4-yl}carbonyl)amino]-3-{[(3R,4S,5S)-6-{[(2S)-1-({2-[(4'R)-4-{[(3E)-3-amino-3-iminopropyl]carbamoyl}-4',5'-dihydro-2,4'-bi-1,3-thiazol-2'-yl]ethyl}amino)-3-hydroxy-3-methyl-1-oxobutan-2-yl]amino}-1,4-dihydroxy-5-methyl-6-oxohexan-3-yl]amino}-1-(1H-imidazol-4-yl)-3-oxopropyl]oxy}-4,5-dihydroxy-6-methyltetrahydro-2H-pyran-3-yl]oxy}-3,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-4-yl carbamate (non-preferred name)

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Chemical information

Composition
Formula: C55H85N19O21S2 / Number of atoms: 182 / Formula weight: 1412.508 / Formal charge: 0
Others

5cj3

Type: NON-POLYMER / PDB classification: HETAD / Three letter code: 52G / Ideal coordinates details: Corina / Model coordinates PDB-ID: 5CJ3
History
Create componentJul 15, 2015
Initial releaseJul 22, 2015
Modify synonymsMar 13, 2021
External linksUniChem / ChemSpider / ChEBI / ChemicalBook / CompTox / Metabolights / NMRShiftDB / Nikkaji / PubChem / 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 12.01O=C(C(CNC(CC(=O)N)c1nc(c(c(N)n1)C)C(=O)NC(C(OC3C(OC2C(C(OC(N)=O)C(O)C(CO)O2)O)C(O)C(O)C(C)O3)c4ncnc4)C(=O)NC(CCO)C(O)C(C)C(=O)NC(C(C)(C)O)C(=O)NCCC5=NC(CS5)c6nc(cs6)C(=O)NCC\C(=N)N)N)N
CACTVS 3.385C[CH]1O[CH](O[CH]([CH](NC(=O)c2nc(nc(N)c2C)[CH](CC(N)=O)NC[CH](N)C(N)=O)C(=O)N[CH](CCO)[CH](O)[CH](C)C(=O)N[CH](C(=O)NCCC3=N[CH](CS3)c4scc(n4)C(=O)NCCC(N)=N)C(C)(C)O)c5c[nH]cn5)[CH](O[CH]6O[CH](CO)[CH](O)[CH](OC(N)=O)[CH]6O)[CH](O)[CH]1O
OpenEye OEToolkits 1.9.2Cc1c(nc(nc1N)C(CC(=O)N)NCC(C(=O)N)N)C(=O)NC(C(c2c[nH]cn2)OC3C(C(C(C(O3)C)O)O)OC4C(C(C(C(O4)CO)O)OC(=O)N)O)C(=O)NC(CCO)C(C(C)C(=O)NC(C(=O)NCCC5=NC(CS5)c6nc(cs6)C(=O)NCCC(=N)N)C(C)(C)O)O

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SMILES CANONICAL

CACTVS 3.385C[C@@H]1O[C@@H](O[C@H]([C@H](NC(=O)c2nc(nc(N)c2C)[C@H](CC(N)=O)NC[C@H](N)C(N)=O)C(=O)N[C@H](CCO)[C@@H](O)[C@H](C)C(=O)N[C@H](C(=O)NCCC3=N[C@H](CS3)c4scc(n4)C(=O)NCCC(N)=N)C(C)(C)O)c5c[nH]cn5)[C@@H](O[C@H]6O[C@H](CO)[C@@H](O)[C@H](OC(N)=O)[C@@H]6O)[C@@H](O)[C@@H]1O
OpenEye OEToolkits 1.9.2[H]/N=C(\CCNC(=O)c1csc(n1)[C@H]2CSC(=N2)CCNC(=O)[C@H](C(C)(C)O)NC(=O)[C@@H](C)[C@@H]([C@@H](CCO)NC(=O)[C@H]([C@H](c3c[nH]cn3)O[C@H]4[C@H]([C@H]([C@@H]([C@@H](O4)C)O)O)O[C@@H]5[C@H]([C@H]([C@@H]([C@H](O5)CO)O)OC(=O)N)O)NC(=O)c6c(c(nc(n6)[C@H](CC(=O)N)NC[C@@H](C(=O)N)N)N)C)O)/N

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InChI

InChI 1.03InChI=1S/C55H85N19O21S2/c1-19-32(71-45(74-43(19)60)24(12-30(59)77)66-13-22(56)44(61)83)48(86)72-33(39(25-14-63-18-67-25)93-53-41(37(81)35(79)21(3)91-53)94-52-38(82)40(95-54(62)89)36(80)28(15-76)92-52)49(87)69-23(8-11-75)34(78)20(2)46(84)73-42(55(4,5)90)50(88)65-10-7-31-68-27(17-96-31)51-70-26(16-97-51)47(85)64-9-6-29(57)58/h14,16,18,20-24,27-28,33-42,52-53,66,75-76,78-82,90H,6-13,15,17,56H2,1-5H3,(H3,57,58)(H2,59,77)(H2,61,83)(H2,62,89)(H,63,67)(H,64,85)(H,65,88)(H,69,87)(H,72,86)(H,73,84)(H2,60,71,74)/t20-,21-,22-,23+,24-,27+,28+,33-,34-,35+,36+,37-,38-,39-,40-,41-,42+,52+,53-/m0/s1

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InChIKey

InChI 1.03UJKRUPHWCPAJIL-CPLCKGKLSA-N

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SYSTEMATIC NAME

ACDLabs 12.01(2R,3S,4S,5R,6R)-2-{[(2R,3S,4S,5S,6S)-2-{[(1R,2S)-2-[({6-amino-2-[(1S)-3-amino-1-{[(2S)-2,3-diamino-3-oxopropyl]amino}-3-oxopropyl]-5-methylpyrimidin-4-yl}carbonyl)amino]-3-{[(3R,4S,5S)-6-{[(2S)-1-({2-[(4'R)-4-{[(3E)-3-amino-3-iminopropyl]carbamoyl}-4',5'-dihydro-2,4'-bi-1,3-thiazol-2'-yl]ethyl}amino)-3-hydroxy-3-methyl-1-oxobutan-2-yl]amino}-1,4-dihydroxy-5-methyl-6-oxohexan-3-yl]amino}-1-(1H-imidazol-4-yl)-3-oxopropyl]oxy}-4,5-dihydroxy-6-methyltetrahydro-2H-pyran-3-yl]oxy}-3,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-4-yl carbamate (non-preferred name)
OpenEye OEToolkits 1.9.2[(2R,3S,4S,5R,6R)-2-[(2R,3S,4S,5S,6S)-2-[(1R,2S)-2-[[6-azanyl-2-[(1S)-3-azanyl-1-[[(2S)-2,3-bis(azanyl)-3-oxidanylidene-propyl]amino]-3-oxidanylidene-propyl]-5-methyl-pyrimidin-4-yl]carbonylamino]-3-[[(3R,4S,5S)-6-[[(2S)-1-[2-[(4R)-4-[4-[(3-azanyl-3-azanylidene-propyl)carbamoyl]-1,3-thiazol-2-yl]-4,5-dihydro-1,3-thiazol-2-yl]ethylamino]-3-methyl-3-oxidanyl-1-oxidanylidene-butan-2-yl]amino]-5-methyl-1,4-bis(oxidanyl)-6-oxidanylidene-hexan-3-yl]amino]-1-(1H-imidazol-4-yl)-3-oxidanylidene-propoxy]-6-methyl-4,5-bis(oxidanyl)oxan-3-yl]oxy-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-4-yl] carbamate

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PDB entries

Showing all 1 items

PDB-5cj3:
Crystal structure of the zorbamycin binding protein (ZbmA) from Streptomyces flavoviridis with zorbamycin

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