Pacidamycin I

    WARNING: This product is for research use only, not for human or veterinary use.

MedKoo CAT#: 571166

CAS#: 121264-05-9

Description: Pacidamycin I is an antimicrobial nucleoside antibiotics that acts by inhibiting the clinically unexploited target translocase I, a key enzyme in peptidoglycan assembly. It is an essential pharmacophore isolated from Streptomyces coeruleorubidus.

Price and Availability




Pacidamycin I is not in stock, may be available through custom synthesis. For cost-effective reason, minimum 1 gram order is requested. The product will be characterized by NMR, HPLC and MS analysis. Purity (HPLC) is usually >98%. CoA, QC data, MSDS will be provided when product is successfully made. The estimated lead time is 2-3 months. Please send email to to inquire quote.

Chemical Structure


Theoretical Analysis

MedKoo Cat#: 571166
Name: Pacidamycin I
CAS#: 121264-05-9
Chemical Formula: C41H50N10O12
Exact Mass: 874.361
Molecular Weight: 874.91
Elemental Analysis: C, 56.29; H, 5.76; N, 16.01; O, 21.94

Synonym: Pacidamycin I; A 68567; A-68567; A68567

IUPAC/Chemical Name: Butanamide, N-(((1-carboxy-2-(1H-indol-3-yl)ethyl)amino)carbonyl)alanyl-N3-(N-alanyl-3-hydroxyphenylalanyl)-N-((5-(3,4-dihydro-2,4-dioxo-1(2H)-pyrimidinyl)dihydro-4-hydroxy-2(3H)-furanylidene)methyl)-N3-methyl-2,3-diamino-


InChi Code: InChI=1S/C41H50N10O12/c1-20(42)34(55)46-29(15-23-8-7-9-25(52)14-23)36(57)49(4)22(3)33(43)37(58)51(19-26-17-31(53)38(63-26)50-13-12-32(54)48-41(50)62)35(56)21(2)45-40(61)47-30(39(59)60)16-24-18-44-28-11-6-5-10-27(24)28/h5-14,18-22,29-31,33,38,44,52-53H,15-17,42-43H2,1-4H3,(H,46,55)(H,59,60)(H2,45,47,61)(H,48,54,62)/b26-19+/t20-,21-,22?,29-,30?,31?,33?,38?/m0/s1

SMILES Code: CC(N(C([C@H](CC1=CC=CC(O)=C1)NC([C@H](C)N)=O)=O)C)C(N)C(N(C([C@H](C)NC(NC(C(O)=O)CC2=CNC3=C2C=CC=C3)=O)=O)/C=C4OC(N(C(N5)=O)C=CC5=O)C(O)C/4)=O

Technical Data

Solid powder

>98% (or refer to the Certificate of Analysis)

Shipping Condition:
Shipped under ambient temperature as non-hazardous chemical. This product is stable enough for a few weeks during ordinary shipping and time spent in Customs.

Storage Condition:
Dry, dark and at 0 - 4 C for short term (days to weeks) or -20 C for long term (months to years).

Soluble in DMSO

Shelf Life:
>2 years if stored properly

Drug Formulation:
This drug may be formulated in DMSO

Stock Solution Storage:
0 - 4 C for short term (days to weeks), or -20 C for long term (months).

Harmonized System Code:


1: Okamoto K, Sakagami M, Feng F, Togame H, Takemoto H, Ichikawa S, Matsuda A. Total synthesis of pacidamycin D by Cu(I)-catalyzed oxy enamide formation. Org Lett. 2011 Oct 7;13(19):5240-3. doi: 10.1021/ol202124b. Epub 2011 Sep 8. PubMed PMID: 21902200.

2: Ragab AE, Grüschow S, Tromans DR, Goss RJ. Biogenesis of the unique 4',5'-dehydronucleoside of the uridyl peptide antibiotic pacidamycin. J Am Chem Soc. 2011 Oct 5;133(39):15288-91. doi: 10.1021/ja206163j. Epub 2011 Sep 12. PubMed PMID: 21861518.

3: Tromans DR, Stevenson CE, Goss RJ, Lawson DM. Crystallization and preliminary X-ray analysis of Pac17 from the pacidamycin-biosynthetic cluster of Streptomyces coeruleorubidus. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 Aug 1;68(Pt 8):971-4. doi: 10.1107/S1744309112029144. Epub 2012 Jul 31. PubMed PMID: 22869135; PubMed Central PMCID: PMC3412786.

4: Boojamra CG, Lemoine RC, Lee JC, Léger R, Stein KA, Vernier NG, Magon A, Lomovskaya O, Martin PK, Chamberland S, Lee MD, Hecker SJ, Lee VJ. Stereochemical elucidation and total synthesis of dihydropacidamycin D, a semisynthetic pacidamycin. J Am Chem Soc. 2001 Feb 7;123(5):870-4. PubMed PMID: 11456620.

5: Zhang W, Ntai I, Bolla ML, Malcolmson SJ, Kahne D, Kelleher NL, Walsh CT. Nine enzymes are required for assembly of the pacidamycin group of peptidyl nucleoside antibiotics. J Am Chem Soc. 2011 Apr 13;133(14):5240-3. doi: 10.1021/ja2011109. Epub 2011 Mar 18. PubMed PMID: 21417270; PubMed Central PMCID: PMC3071879.

6: Zhang W, Ntai I, Kelleher NL, Walsh CT. tRNA-dependent peptide bond formation by the transferase PacB in biosynthesis of the pacidamycin group of pentapeptidyl nucleoside antibiotics. Proc Natl Acad Sci U S A. 2011 Jul 26;108(30):12249-53. doi: 10.1073/pnas.1109539108. Epub 2011 Jul 11. PubMed PMID: 21746899; PubMed Central PMCID: PMC3145694.

7: Rackham EJ, Grüschow S, Ragab AE, Dickens S, Goss RJ. Pacidamycin biosynthesis: identification and heterologous expression of the first uridyl peptide antibiotic gene cluster. Chembiochem. 2010 Aug 16;11(12):1700-9. doi: 10.1002/cbic.201000200. PubMed PMID: 20665770.

8: Mistry A, Warren MS, Cusick JK, Karkhoff-Schweizer RR, Lomovskaya O, Schweizer HP. High-level pacidamycin resistance in Pseudomonas aeruginosa is mediated by an opp oligopeptide permease encoded by the opp-fabI operon. Antimicrob Agents Chemother. 2013 Nov;57(11):5565-71. doi: 10.1128/AAC.01198-13. Epub 2013 Aug 26. PubMed PMID: 23979749; PubMed Central PMCID: PMC3811240.

9: Okamoto K, Sakagami M, Feng F, Togame H, Takemoto H, Ichikawa S, Matsuda A. Total synthesis and biological evaluation of pacidamycin D and its 3'-hydroxy analogue. J Org Chem. 2012 Feb 3;77(3):1367-77. doi: 10.1021/jo202159q. Epub 2012 Jan 18. PubMed PMID: 22196045.

10: Rackham EJ, Grüschow S, Goss RJ. Revealing the first uridyl peptide antibiotic biosynthetic gene cluster and probing pacidamycin biosynthesis. Bioeng Bugs. 2011 Jul-Aug;2(4):218-21. doi: 10.4161/bbug.2.4.15877. Epub 2011 Jul 1. PubMed PMID: 21829097; PubMed Central PMCID: PMC3225657.

11: Grüschow S, Rackham EJ, Elkins B, Newill PL, Hill LM, Goss RJ. New pacidamycin antibiotics through precursor-directed biosynthesis. Chembiochem. 2009 Jan 26;10(2):355-60. doi: 10.1002/cbic.200800575. PubMed PMID: 19090518.

12: Karwowski JP, Jackson M, Theriault RJ, Chen RH, Barlow GJ, Maus ML. Pacidamycins, a novel series of antibiotics with anti-Pseudomonas aeruginosa activity. I. Taxonomy of the producing organism and fermentation. J Antibiot (Tokyo). 1989 Apr;42(4):506-11. PubMed PMID: 2498263.

13: Deb Roy A, Grüschow S, Cairns N, Goss RJ. Gene expression enabling synthetic diversification of natural products: chemogenetic generation of pacidamycin analogs. J Am Chem Soc. 2010 Sep 8;132(35):12243-5. doi: 10.1021/ja1060406. PubMed PMID: 20712319.

14: Zhang W, Heemstra JR Jr, Walsh CT, Imker HJ. Activation of the pacidamycin PacL adenylation domain by MbtH-like proteins. Biochemistry. 2010 Nov 23;49(46):9946-7. doi: 10.1021/bi101539b. Epub 2010 Nov 1. PubMed PMID: 20964365; PubMed Central PMCID: PMC2982891.

15: Zhang W, Ostash B, Walsh CT. Identification of the biosynthetic gene cluster for the pacidamycin group of peptidyl nucleoside antibiotics. Proc Natl Acad Sci U S A. 2010 Sep 28;107(39):16828-33. doi: 10.1073/pnas.1011557107. Epub 2010 Sep 8. PubMed PMID: 20826445; PubMed Central PMCID: PMC2947877.

16: Fernandes PB, Swanson RN, Hardy DJ, Hanson CW, Coen L, Rasmussen RR, Chen RH. Pacidamycins, a novel series of antibiotics with anti-Pseudomonas aeruginosa activity. III. Microbiologic profile. J Antibiot (Tokyo). 1989 Apr;42(4):521-6. PubMed PMID: 2498265.

17: Chen RH, Buko AM, Whittern DN, McAlpine JB. Pacidamycins, a novel series of antibiotics with anti-Pseudomonas aeruginosa activity. II. Isolation and structural elucidation. J Antibiot (Tokyo). 1989 Apr;42(4):512-20. PubMed PMID: 2498264.

18: Fronko RM, Lee JC, Galazzo JG, Chamberland S, Malouin F, Lee MD. New pacidamycins produced by Streptomyces coeruleorubidus, NRRL 18370. J Antibiot (Tokyo). 2000 Dec;53(12):1405-10. PubMed PMID: 11217807.

19: Boojamra CG, Lemoine RC, Blais J, Vernier NG, Stein KA, Magon A, Chamberland S, Hecker SJ, Lee VJ. Synthetic dihydropacidamycin antibiotics: a modified spectrum of activity for the pacidamycin class. Bioorg Med Chem Lett. 2003 Oct 6;13(19):3305-9. PubMed PMID: 12951115.

20: Winn M, Goss RJ, Kimura K, Bugg TD. Antimicrobial nucleoside antibiotics targeting cell wall assembly: recent advances in structure-function studies and nucleoside biosynthesis. Nat Prod Rep. 2010 Feb;27(2):279-304. doi: 10.1039/b816215h. Epub 2009 Dec 16. Review. PubMed PMID: 20111805.