NPASS Compound

Natural Product: NPC477329

Natural Product ID	NPC477329
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Murucin 2
IUPAC Name	[(2S,3R,4R,5R,6S)-4-hydroxy-5-[(2S,3R,4R,5R,6S)-4-hydroxy-6-methyl-5-propanoyloxy-3-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyoxan-2-yl]oxy-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 2
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	44559237
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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67 1 0 64 68 1 0 68 69 1 0 69 70 2 0 69 71 1 0 71 72 1 0 63 73 1 0 62 74 1 0 74 75 1 0 75 76 1 0 76 77 1 0 77 78 1 0 78 79 1 0 79 80 1 0 79 81 1 0 81 82 1 0 78 83 1 0 77 84 1 0 76 85 1 0 16 86 1 0 20 15 1 0 27 22 1 0 45 25 1 0 49 43 1 0 66 61 1 0 80 75 1 0 1 87 1 0 1 88 1 0 1 89 1 0 2 90 1 0 2 91 1 0 3 92 1 0 3 93 1 0 4 94 1 0 4 95 1 0 5 96 1 0 5 97 1 0 6 98 1 0 6 99 1 0 7100 1 0 7101 1 0 8102 1 0 8103 1 0 9104 1 0 9105 1 0 10106 1 0 10107 1 0 11108 1 0 11109 1 0 15110 1 6 16111 1 6 17112 1 1 18113 1 6 20114 1 1 22115 1 1 23116 1 6 25117 1 0 26118 1 6 27119 1 6 28120 1 0 32121 1 0 32122 1 0 33123 1 0 33124 1 0 34125 1 0 34126 1 0 35127 1 0 35128 1 0 36129 1 0 36130 1 0 37131 1 0 37132 1 0 38133 1 0 38134 1 0 39135 1 0 39136 1 0 40137 1 0 40138 1 0 41139 1 0 43140 1 1 44141 1 6 46142 1 1 47143 1 6 48144 1 1 50145 1 0 50146 1 0 50147 1 0 51148 1 0 52149 1 0 53150 1 0 53151 1 0 54152 1 0 54153 1 0 55154 1 0 55155 1 0 56156 1 0 56157 1 0 57158 1 0 57159 1 0 57160 1 0 58161 1 0 58162 1 0 58163 1 0 59164 1 0 59165 1 0 59166 1 0 61167 1 1 62168 1 6 63169 1 6 64170 1 1 65171 1 6 67172 1 0 67173 1 0 67174 1 0 71175 1 0 71176 1 0 72177 1 0 72178 1 0 72179 1 0 73180 1 0 75181 1 1 76182 1 6 77183 1 1 78184 1 6 79185 1 1 81186 1 0 81187 1 0 82188 1 0 83189 1 0 84190 1 0 85191 1 0 86192 1 0 M END

Standard InCHIKey	RYIDWTWUNMIANO-YQIHXUGCSA-N
Standard InCHI	InChI=1S/C61H106O25/c1-8-11-13-14-15-16-19-22-26-30-40(64)81-54-48(72)52(84-61-56(47(71)50(34(5)75-61)80-39(63)10-3)85-57-46(70)44(68)43(67)38(32-62)79-57)35(6)76-59(54)83-51-36(7)77-60-55(49(51)73)82-41(65)31-27-23-20-17-18-21-25-29-37(28-24-12-9-2)78-58-53(86-60)45(69)42(66)33(4)74-58/h33-38,42-62,66-73H,8-32H2,1-7H3/t33-,34+,35+,36+,37?,38-,42-,43-,44+,45+,46-,47-,48-,49-,50+,51+,52+,53-,54-,55-,56-,57+,58+,59+,60?,61+/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)CC)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:	1238.7	Volume:	1224.119 ? Van der Waals volume.
Dense:	1.012	LogP:	5.049 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	4.502 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.064 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	26.0	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:	0.038	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	7.295	Fsp³:	0.951
MCE-18:	121.647 ? 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:	0.994	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:	0.002 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.515	Promiscuous compounds:	0.069

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.515	MDCK Permeability:	-5.007
Pgp-inhibitor:	0.0	Pgp-substrate:	0.756
PAMPA:	0.535 ? 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):	0.022
20% Bioavailability (F20%):	0.001	30% Bioavailability (F30%):	0.825
50% Bioavailability (F50%):	0.975

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.989
Plasma Protein Binding (PPB):	92.964%	Volume Distribution (VD):	-0.192
Fu:	5.267% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.0
BSEP inhibitor:	0.946

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:	1.0
HLM stability:	0.894 ? 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):

0.616

Half-life (T1/2):

3.526

ADMET: Toxicity

hERG Blockers:	0.034	hERG Blockers (10um):	0.101
Human Hepatotoxicity (H-HT):	0.285	Drug-induced Liver Injury (DILI):	0.977
AMES Toxicity:	0.286	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:	0.328	Drug-induced Nephrotoxicity:	0.843
Genotoxicity:	0.0	RPMI-8226 Immunitoxicity:	0.388
A549 Cytotoxicity:	0.985	Hek293 Cytotoxicity:	0.265
BCF:	0.71 ? 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:	4.485 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.179 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.8 ? 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	3

Activity Type	# Activity
Cell line	2
Others	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	>	20	ug/ml	PMID[16124750]
NPT148	Cell line	HCT-15	Homo sapiens	ED50	>	20	ug/ml	PMID[16124750]
NPT2	Others	Unspecified	n.a.	ED50	>	20	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 NPC477329 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	24051
0.1-0.2	21507
0.2-0.3	3614
0.3-0.4	523
0.4-0.5	62
0.5-0.6	45
0.6-0.7	44
0.7-0.8	0
0.8-0.85	0
0.85-0.9	2
0.9-0.95	2
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.9552	High Similarity	NPC477330
0.9265	High Similarity	NPC477328
0.9242	High Similarity	NPC478729
0.863	High Similarity	NPC477331
0.863	High Similarity	NPC477332
0.7922	Intermediate Similarity	NPC109887
0.716	Intermediate Similarity	NPC478722
0.7143	Intermediate Similarity	NPC224953
0.7073	Intermediate Similarity	NPC478724
0.7033	Intermediate Similarity	NPC28069
0.7	Intermediate Similarity	NPC89843
0.6974	Remote Similarity	NPC477350
0.6914	Remote Similarity	NPC600446
0.6914	Remote Similarity	NPC605013
0.6897	Remote Similarity	NPC478728
0.6875	Remote Similarity	NPC604005
0.6875	Remote Similarity	NPC605014
0.6818	Remote Similarity	NPC478727
0.6747	Remote Similarity	NPC478725
0.6744	Remote Similarity	NPC184915
0.6707	Remote Similarity	NPC477326
0.6667	Remote Similarity	NPC475425
0.6667	Remote Similarity	NPC478723
0.6591	Remote Similarity	NPC44782
0.6588	Remote Similarity	NPC119583
0.6543	Remote Similarity	NPC477349
0.6512	Remote Similarity	NPC478726
0.6471	Remote Similarity	NPC206823
0.6437	Remote Similarity	NPC169345
0.6437	Remote Similarity	NPC115013
0.6395	Remote Similarity	NPC472204
0.6353	Remote Similarity	NPC146992
0.6353	Remote Similarity	NPC85759
0.6353	Remote Similarity	NPC479061
0.6341	Remote Similarity	NPC22742
0.6341	Remote Similarity	NPC477346
0.6322	Remote Similarity	NPC483170
0.6316	Remote Similarity	NPC77651
0.6296	Remote Similarity	NPC281563
0.6289	Remote Similarity	NPC290276
0.6279	Remote Similarity	NPC479060
0.625	Remote Similarity	NPC146380
0.6207	Remote Similarity	NPC294748
0.618	Remote Similarity	NPC183888
0.618	Remote Similarity	NPC126685
0.6145	Remote Similarity	NPC87153
0.6145	Remote Similarity	NPC113745
0.6145	Remote Similarity	NPC477320
0.6145	Remote Similarity	NPC477323
0.6145	Remote Similarity	NPC477325
0.6145	Remote Similarity	NPC609436
0.6111	Remote Similarity	NPC163409
0.6111	Remote Similarity	NPC472200
0.6067	Remote Similarity	NPC238056
0.6044	Remote Similarity	NPC269318
0.5977	Remote Similarity	NPC60849
0.5909	Remote Similarity	NPC472205
0.5889	Remote Similarity	NPC477317
0.5889	Remote Similarity	NPC477318
0.5875	Remote Similarity	NPC606819
0.5824	Remote Similarity	NPC259294
0.5814	Remote Similarity	NPC478734
0.5795	Remote Similarity	NPC267592
0.5769	Remote Similarity	NPC471026
0.5747	Remote Similarity	NPC477344
0.573	Remote Similarity	NPC477319
0.5727	Remote Similarity	NPC147032
0.5686	Remote Similarity	NPC471025
0.5682	Remote Similarity	NPC478733
0.5667	Remote Similarity	NPC143421
0.5667	Remote Similarity	NPC307400
0.5667	Remote Similarity	NPC27289
0.5556	Remote Similarity	NPC297768
0.5543	Remote Similarity	NPC162925
0.5543	Remote Similarity	NPC290012
0.5493	Remote Similarity	NPC241265
0.549	Remote Similarity	NPC10883
0.5435	Remote Similarity	NPC238264
0.5435	Remote Similarity	NPC477345
0.5426	Remote Similarity	NPC123204
0.5385	Remote Similarity	NPC44682
0.5377	Remote Similarity	NPC600940
0.537	Remote Similarity	NPC471024
0.5352	Remote Similarity	NPC76881
0.534	Remote Similarity	NPC10121
0.534	Remote Similarity	NPC198918
0.5319	Remote Similarity	NPC479057
0.5222	Remote Similarity	NPC158302
0.5222	Remote Similarity	NPC479059
0.5217	Remote Similarity	NPC173328
0.5208	Remote Similarity	NPC477347
0.5204	Remote Similarity	NPC477348
0.5185	Remote Similarity	NPC472352
0.5161	Remote Similarity	NPC186992
0.5152	Remote Similarity	NPC475241
0.5065	Remote Similarity	NPC163812
0.5055	Remote Similarity	NPC216883
0.5054	Remote Similarity	NPC479058
0.5054	Remote Similarity	NPC476781
0.5048	Remote Similarity	NPC611287

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC477329 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7388
0.1-0.2	1657
0.2-0.3	93
0.3-0.4	12
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