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ramoplanin A2   Click here for help

GtoPdb Ligand ID: 14348

Synonyms: A-16686A2 | MDL 62,198
Compound class: Peptide
Comment: Ramoplanin is a glycolipodepsipeptide antibacterial with Gram-positive activity, originally isolated from the culture broth of Actinoplanes strain ATCC 33076 as a mixture of three components (ramoplanin A1, A2, and A3) [1,3].
We show the structure for ramoplanin A2 which is the major component. Note that the INN describes the mixture. As with other natural products, there is ambiguity in the precise stereochemisrty presented across web resources e.g., CHEMBL3989605 shows an alternate structure.
2D Structure
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2D Structure

An image of the ligand's 2D structure. For small molecules with SMILES these are drawn using the NCI/CADD Chemical Identifier Resolver. Click on the image to access the chemical structure search tool with the ligand pre-loaded in the structure editor. For other types of ligands, e.g. longer nucleotides and peptides, a manually drawn representation of the molecule may be provided.

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SMILES / InChI / InChIKey
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SMILES / InChI / InChIKey

SMILES (Simplified Molecular Input Line Entry Specification) A specification for unambiguously describing the structure of chemical molecules using short ASCII strings. Canonical SMILES specify a unique representation of the 2D structure without chiral or isotopic specifications. Isomeric SMILES include chiral specification and isotopes.

Standard InChI (IUPAC International Chemical Identifier) and InChIKey InChI is a non-proprietary, standard, textual identifier for chemical substances designed to facilitate linking of information and database searching. An InChIKey is a simplified version of a full InChI, designed for easier web searching.

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)

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Canonical SMILES CC(C)C/C=C/C=C\C(=O)N[C@@H](CC(=O)N)C(=O)N[C@H]1[C@@H](C(=O)N)OC(=O)[C@H](C2=CC=C(C(=C2)Cl)O)NC(=O)[C@@H](C)NC(=O)[C@H](CC(C)C)NC(=O)CNC(=O)[C@H](C3=CC=C(C=C3)O)NC(=O)[C@@H]([C@@H](C)O)NC(=O)[C@H](C4=CC=C(C=C4)O[C@@H]5[C@H]([C@H]([C@@H]([C@@H](CO)O5)O)O)O[C@@H]6[C@H]([C@H]([C@@H]([C@@H](CO)O6)O)O)O)NC(=O)[C@@H](CCCN)NC(=O)[C@H](CC7=CC=CC=C7)NC(=O)[C@H]([C@H](C)O)NC(=O)[C@@H](C8=CC=C(C=C8)O)NC(=O)[C@H](C9=CC=C(C=C9)O)NC(=O)[C@@H]([C@@H](C)O)NC(=O)[C@@H](CCCN)NC(=O)[C@@H](C%10=CC=C(C=C%10)O)NC1=O
Isomeric SMILES C[C@@H]1C(=O)N[C@H](C(=O)O[C@@H]([C@@H](C(=O)N[C@@H](C(=O)N[C@@H](C(=O)N[C@@H](C(=O)N[C@H](C(=O)N[C@@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@@H](C(=O)N[C@H](C(=O)N[C@@H](C(=O)N[C@H](C(=O)NCC(=O)N[C@H](C(=O)N1)CC(C)C)C2=CC=C(C=C2)O)[C@@H](C)O)C3=CC=C(C=C3)O[C@@H]4[C@H]([C@H]([C@@H]([C@H](O4)CO)O)O)O[C@@H]5[C@H]([C@H]([C@@H]([C@H](O5)CO)O)O)O)CCCN)CC6=CC=CC=C6)[C@H](C)O)C7=CC=C(C=C7)O)C8=CC=C(C=C8)O)[C@@H](C)O)CCCN)C9=CC=C(C=C9)O)NC(=O)[C@H](CC(=O)N)NC(=O)/C=C\C=C\CC(C)C)C(=O)N)C%10=CC(=C(C=C%10)O)Cl
InChI InChI=1S/C119H154ClN21O40/c1-54(2)17-11-9-14-22-82(153)127-77(50-81(123)152)107(166)141-93-99(101(124)160)180-117(176)92(66-33-44-78(151)72(120)49-66)140-102(161)56(5)126-105(164)75(47-55(3)4)128-83(154)51-125-108(167)87(61-23-34-67(147)35-24-61)136-111(170)86(59(8)146)134-113(172)89(65-31-42-71(43-32-65)177-119-100(97(158)95(156)80(53-143)179-119)181-118-98(159)96(157)94(155)79(52-142)178-118)135-104(163)73(20-15-45-121)129-106(165)76(48-60-18-12-10-13-19-60)131-109(168)84(57(6)144)133-114(173)90(63-27-38-69(149)39-28-63)138-115(174)91(64-29-40-70(150)41-30-64)137-110(169)85(58(7)145)132-103(162)74(21-16-46-122)130-112(171)88(139-116(93)175)62-25-36-68(148)37-26-62/h9-14,18-19,22-44,49,54-59,73-77,79-80,84-100,118-119,142-151,155-159H,15-17,20-21,45-48,50-53,121-122H2,1-8H3,(H2,123,152)(H2,124,160)(H,125,167)(H,126,164)(H,127,153)(H,128,154)(H,129,165)(H,130,171)(H,131,168)(H,132,162)(H,133,173)(H,134,172)(H,135,163)(H,136,170)(H,137,169)(H,138,174)(H,139,175)(H,140,161)(H,141,166)/b11-9+,22-14-/t56-,57+,58-,59-,73-,74-,75+,76+,77+,79-,80-,84+,85-,86-,87+,88-,89+,90-,91+,92+,93+,94-,95-,96+,97+,98+,99+,100+,118-,119+/m1/s1
InChI Key KGZHFKDNSAEOJX-WIFQYKSHSA-N

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
References
1. Cavalleri B, Pagani H, Volpe G, Selva E, Parenti F. (1984)
A-16686, a new antibiotic from Actinoplanes. I. Fermentation, isolation and preliminary physico-chemical characteristics.
J Antibiot (Tokyo), 37 (4): 309-17. [PMID:6547132]
2. Fang X, Tiyanont K, Zhang Y, Wanner J, Boger D, Walker S. (2006)
The mechanism of action of ramoplanin and enduracidin.
Mol Biosyst, 2 (1): 69-76. [PMID:16880924]
3. Pallanza R, Berti M, Scotti R, Randisi E, Arioli V. (1984)
A-16686, a new antibiotic from Actinoplanes. II. Biological properties.
J Antibiot (Tokyo), 37 (4): 318-24. [PMID:6547133]
4. Wong MT, Kauffman CA, Standiford HC, Linden P, Fort G, Fuchs HJ, Porter SB, Wenzel RP, Ramoplanin VRE2 Clinival Stury Group. (2001)
Effective suppression of vancomycin-resistant Enterococcus species in asymptomatic gastrointestinal carriers by a novel glycolipodepsipeptide, ramoplanin.
Clin Infect Dis, 33 (9): 1476-82. [PMID:11588692]
5. Zorzet A. (2014)
Overcoming scientific and structural bottlenecks in antibacterial discovery and development.
Ups J Med Sci, 119 (2): 170-5. [PMID:24646118]