NPASS Compound

Natural Product: NPC477328

Natural Product ID	NPC477328
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Murucin 1
IUPAC Name	[(2S,3R,4R,5R,6S)-5-[(2S,3R,4R,5R,6S)-5-acetyloxy-4-hydroxy-6-methyl-3-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyoxan-2-yl]oxy-4-hydroxy-6-methyl-2-[[(1R,5S,6R,7R,8R,22R,24R,25S,26S)-7,25,26-trihydroxy-5,24-dimethyl-10-oxo-20-pentyl-2,4,9,21,23-pentaoxatricyclo[20.4.0.03,8]hexacosan-6-yl]oxy]oxan-3-yl] dodecanoate
Synonyms	Murucin 1
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	44559236
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates [CHEMONTID:0000198] Oligosaccharides

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

Chemical Representations

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82 1 0 76 83 1 0 75 84 1 0 16 85 1 0 20 15 1 0 27 22 1 0 45 25 1 0 49 43 1 0 66 61 1 0 79 74 1 0 1 86 1 0 1 87 1 0 1 88 1 0 2 89 1 0 2 90 1 0 3 91 1 0 3 92 1 0 4 93 1 0 4 94 1 0 5 95 1 0 5 96 1 0 6 97 1 0 6 98 1 0 7 99 1 0 7100 1 0 8101 1 0 8102 1 0 9103 1 0 9104 1 0 10105 1 0 10106 1 0 11107 1 0 11108 1 0 15109 1 6 16110 1 6 17111 1 1 18112 1 6 20113 1 1 22114 1 1 23115 1 6 25116 1 0 26117 1 6 27118 1 6 28119 1 0 32120 1 0 32121 1 0 33122 1 0 33123 1 0 34124 1 0 34125 1 0 35126 1 0 35127 1 0 36128 1 0 36129 1 0 37130 1 0 37131 1 0 38132 1 0 38133 1 0 39134 1 0 39135 1 0 40136 1 0 40137 1 0 41138 1 0 43139 1 1 44140 1 6 46141 1 1 47142 1 6 48143 1 1 50144 1 0 50145 1 0 50146 1 0 51147 1 0 52148 1 0 53149 1 0 53150 1 0 54151 1 0 54152 1 0 55153 1 0 55154 1 0 56155 1 0 56156 1 0 57157 1 0 57158 1 0 57159 1 0 58160 1 0 58161 1 0 58162 1 0 59163 1 0 59164 1 0 59165 1 0 61166 1 1 62167 1 6 63168 1 6 64169 1 1 65170 1 6 67171 1 0 67172 1 0 67173 1 0 71174 1 0 71175 1 0 71176 1 0 72177 1 0 74178 1 1 75179 1 6 76180 1 1 77181 1 6 78182 1 1 80183 1 0 80184 1 0 81185 1 0 82186 1 0 83187 1 0 84188 1 0 85189 1 0 M END

Standard InCHIKey	TUDUJRAYAQOSHP-NRAIBJJHSA-N
Standard InCHI	InChI=1S/C60H104O25/c1-8-10-12-13-14-15-18-21-25-29-39(63)80-53-47(71)51(83-60-55(46(70)49(33(4)74-60)77-36(7)62)84-56-45(69)43(67)42(66)38(31-61)79-56)34(5)75-58(53)82-50-35(6)76-59-54(48(50)72)81-40(64)30-26-22-19-16-17-20-24-28-37(27-23-11-9-2)78-57-52(85-59)44(68)41(65)32(3)73-57/h32-35,37-38,41-61,65-72H,8-31H2,1-7H3/t32-,33+,34+,35+,37?,38-,41-,42-,43+,44+,45-,46-,47-,48-,49+,50+,51+,52-,53-,54-,55-,56+,57+,58+,59?,60+/m1/s1
SMILES	CCCCCCCCCCCC(=O)O[C@@H]1[C@@H]([C@H]([C@@H](O[C@H]1O[C@H]2[C@@H](OC3[C@@H]([C@@H]2O)OC(=O)CCCCCCCCCC(O[C@H]4[C@H](O3)[C@H]([C@@H]([C@H](O4)C)O)O)CCCCC)C)C)O[C@H]5[C@@H]([C@@H]([C@H]([C@@H](O5)C)OC(=O)C)O)O[C@H]6[C@@H]([C@H]([C@@H]([C@H](O6)CO)O)O)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	1224.69	Volume:	1206.823 ? Van der Waals volume.
Dense:	1.015	LogP:	4.714 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	4.262 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.026 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	25.0	Rigid Bonds:	49.0
TPSA:	353.27 ? Topological Polar Surface Area.	H-Bond Acceptor:	25.0
H-Bond Donor:	9.0	Rings:	6.0
Heavy Atoms:	25.0

MedChem Properties

QED Drug-Likeness Score:	0.04	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	7.261	Fsp³:	0.95
MCE-18:	122.12 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected	GSK Rule:	Accepted
Golden Triangle Rule:	Accepted	BMS Rule:	1
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.989	Fluc inhibitor:	0.333 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.002 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.003 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.485	Promiscuous compounds:	0.123

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.566	MDCK Permeability:	-5.018
Pgp-inhibitor:	0.0	Pgp-substrate:	0.412
PAMPA:	0.726 ? The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).	Human Intestinal Absorption (HIA):	0.042
20% Bioavailability (F20%):	0.001	30% Bioavailability (F30%):	0.944
50% Bioavailability (F50%):	0.97

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.968
Plasma Protein Binding (PPB):	92.777%	Volume Distribution (VD):	-0.183
Fu:	5.497% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.0
BSEP inhibitor:	0.323

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.999
HLM stability:	0.822 ? Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):

0.578

Half-life (T1/2):

3.586

ADMET: Toxicity

hERG Blockers:	0.036	hERG Blockers (10um):	0.115
Human Hepatotoxicity (H-HT):	0.321	Drug-induced Liver Injury (DILI):	0.983
AMES Toxicity:	0.343	Rat Oral Acute Toxicity:	0.0
Maximum Recommended Daily Dose:	0.001	Skin Sensitization:	1.0
Carcinogencity:	0.0	Eye Corrosion:	0.0
Eye Irritation:	0.001	Respiratory Toxicity:	0.0
Drug-induced Neurotoxicity:	0.0	Ototoxicity:	1.0
Hematotoxicity:	0.332	Drug-induced Nephrotoxicity:	0.831
Genotoxicity:	0.0	RPMI-8226 Immunitoxicity:	0.366
A549 Cytotoxicity:	0.988	Hek293 Cytotoxicity:	0.274
BCF:	0.521 ? Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].	IGC50:	4.435 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.076 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.553 ? 96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO2520	Ipomoea murucoides	Species	Convolvulaceae	Eukaryota	Roots	Ixpantepec, in the state of Oaxaca, Mexico	1996-DEC	PMID[16124750]
NPO2520	Ipomoea murucoides	Species	Convolvulaceae	Eukaryota	flowers	n.a.	n.a.	PMID[16643033]
NPO2520	Ipomoea murucoides	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18500841]
NPO2520	Ipomoea murucoides	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]

Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

NP Quantity Composition/Concentration

Organism ID	Organism Name	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

Biological Activity

Activity Type	# Activity
ED50	1

Activity Type	# Activity
Cell line	1

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT382	Cell line	OVCAR-5	Homo sapiens	ED50	=	5	ug/ml	PMID[16124750]

In vivo activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

Experimental ADME

Experiment Model	Experiment Tissue	ADME Type	ADME Relation	ADME Value	ADME Unit	Reference

Experimental Toxicity

Quantitative toxicity

Experiment Model	Experiment Organism	Toxicity Type	Toxicity Relation	Toxicity Value	Toxicity Unit	Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity	Carcinogenicity	Mutagenicity	Cardiotoxicity	Respiratory Toxicity	Eye Irritation	Endocrine Disruption

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]

Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

● The left chart: Distribution of similarity level between NPC477328 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	23893
0.1-0.2	21516
0.2-0.3	3776
0.3-0.4	512
0.4-0.5	61
0.5-0.6	52
0.6-0.7	39
0.7-0.8	0
0.8-0.85	0
0.85-0.9	2
0.9-0.95	3
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.9403	High Similarity	NPC477330
0.9385	High Similarity	NPC478729
0.9265	High Similarity	NPC477329
0.875	High Similarity	NPC477331
0.875	High Similarity	NPC477332
0.7792	Intermediate Similarity	NPC109887
0.725	Intermediate Similarity	NPC478722
0.7229	Intermediate Similarity	NPC224953
0.6977	Remote Similarity	NPC478728
0.6951	Remote Similarity	NPC478723
0.6897	Remote Similarity	NPC478727
0.6875	Remote Similarity	NPC89843
0.6829	Remote Similarity	NPC478725
0.679	Remote Similarity	NPC600446
0.679	Remote Similarity	NPC605013
0.6747	Remote Similarity	NPC478724
0.6628	Remote Similarity	NPC184915
0.6623	Remote Similarity	NPC477350
0.6588	Remote Similarity	NPC478726
0.6585	Remote Similarity	NPC477326
0.6567	Remote Similarity	NPC206823
0.6559	Remote Similarity	NPC28069
0.6552	Remote Similarity	NPC472200
0.6543	Remote Similarity	NPC604005
0.6543	Remote Similarity	NPC605014
0.6538	Remote Similarity	NPC475425
0.6477	Remote Similarity	NPC44782
0.6471	Remote Similarity	NPC119583
0.6429	Remote Similarity	NPC60849
0.642	Remote Similarity	NPC477349
0.6383	Remote Similarity	NPC77651
0.6354	Remote Similarity	NPC290276
0.6322	Remote Similarity	NPC169345
0.6322	Remote Similarity	NPC115013
0.6235	Remote Similarity	NPC479061
0.622	Remote Similarity	NPC22742
0.622	Remote Similarity	NPC477346
0.6207	Remote Similarity	NPC483170
0.6173	Remote Similarity	NPC281563
0.6163	Remote Similarity	NPC479060
0.6092	Remote Similarity	NPC472204
0.6067	Remote Similarity	NPC183888
0.6067	Remote Similarity	NPC126685
0.6047	Remote Similarity	NPC146992
0.6047	Remote Similarity	NPC85759
0.6024	Remote Similarity	NPC87153
0.6	Remote Similarity	NPC163409
0.5977	Remote Similarity	NPC472205
0.5955	Remote Similarity	NPC477317
0.5955	Remote Similarity	NPC477318
0.5926	Remote Similarity	NPC146380
0.5909	Remote Similarity	NPC294748
0.5882	Remote Similarity	NPC478734
0.5833	Remote Similarity	NPC113745
0.5833	Remote Similarity	NPC477320
0.5833	Remote Similarity	NPC477323
0.5833	Remote Similarity	NPC477325
0.5833	Remote Similarity	NPC609436
0.5825	Remote Similarity	NPC471026
0.5814	Remote Similarity	NPC477344
0.5778	Remote Similarity	NPC238056
0.5761	Remote Similarity	NPC269318
0.575	Remote Similarity	NPC606819
0.5747	Remote Similarity	NPC478733
0.5636	Remote Similarity	NPC147032
0.5632	Remote Similarity	NPC479059
0.5618	Remote Similarity	NPC297768
0.5588	Remote Similarity	NPC471025
0.5571	Remote Similarity	NPC241265
0.5543	Remote Similarity	NPC259294
0.5506	Remote Similarity	NPC267592
0.5495	Remote Similarity	NPC238264
0.5495	Remote Similarity	NPC477345
0.5444	Remote Similarity	NPC479058
0.5444	Remote Similarity	NPC477319
0.5435	Remote Similarity	NPC162925
0.5429	Remote Similarity	NPC76881
0.5429	Remote Similarity	NPC600940
0.5405	Remote Similarity	NPC471760
0.5392	Remote Similarity	NPC10883
0.5385	Remote Similarity	NPC143421
0.5385	Remote Similarity	NPC307400
0.5385	Remote Similarity	NPC27289
0.5278	Remote Similarity	NPC471024
0.5269	Remote Similarity	NPC290012
0.5263	Remote Similarity	NPC477347
0.5258	Remote Similarity	NPC477348
0.5213	Remote Similarity	NPC479057
0.5204	Remote Similarity	NPC475241
0.5158	Remote Similarity	NPC123204
0.5132	Remote Similarity	NPC163812
0.5111	Remote Similarity	NPC158302
0.5111	Remote Similarity	NPC216883
0.5109	Remote Similarity	NPC173328
0.5109	Remote Similarity	NPC44682
0.5096	Remote Similarity	NPC10121
0.5096	Remote Similarity	NPC198918
0.5093	Remote Similarity	NPC472352
0.5054	Remote Similarity	NPC186992

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC477328 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7371
0.1-0.2	1681
0.2-0.3	85
0.3-0.4	13
0.4-0.5	0
0.5-0.6	0
0.6-0.7	0
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
		NPD

Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.
Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity

B: biological targets similarity

C: networks similarity

D: cell-based bioactivity similarity

E: similarity based on clinical data