NPASS Compound

Natural Product: NPC123559

Natural Product ID	NPC123559
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	(R,Z)-15-(3,5-Dihydroxyphenyl)Pentadec-7-En-6-Yl Acetate
IUPAC Name	[(Z,6R)-15-(3,5-dihydroxyphenyl)pentadec-7-en-6-yl] acetate
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL478964
PubChem CID	44584498
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0003909] Fatty Acyls [CHEMONTID:0001722] Fatty alcohol esters

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

Chemical Representations

RDKit 3D 63 63 0 0 0 0 0 0 0 0999 V2000 -7.7799 0.8012 -3.3565 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.2848 0.8663 -1.9538 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.5067 -0.0059 -0.9920 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0519 0.3845 -0.9308 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3798 -0.5495 0.0549 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8900 -0.2333 0.1893 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.4097 -1.1855 1.1384 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9079 -0.8444 2.3721 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8602 0.3530 2.7059 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4389 -1.9429 3.2621 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2148 -0.5240 -1.0903 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0608 0.0025 -1.4194 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3211 0.9276 -0.5637 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0655 0.3750 -0.1963 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7131 1.4140 0.6768 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0933 1.0267 1.1299 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0509 0.8030 0.0125 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3920 0.4224 0.5923 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3764 0.1926 -0.5611 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7090 -0.1835 -0.0494 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0363 -1.4968 0.1585 C 0 0 0 0 0 0 0 0 0 0 0 0 8.2858 -1.8773 0.6402 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6504 -3.1948 0.8620 O 0 0 0 0 0 0 0 0 0 0 0 0 9.2077 -0.8882 0.9101 C 0 0 0 0 0 0 0 0 0 0 0 0 8.9096 0.4596 0.7105 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6388 0.7876 0.2247 C 0 0 0 0 0 0 0 0 0 0 0 0 9.8734 1.4126 0.9982 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.6094 0.5000 -4.0368 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.4232 1.8049 -3.7254 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9790 0.0476 -3.5023 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.2030 1.9241 -1.5943 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.3610 0.6055 -1.9006 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.9553 0.0863 0.0025 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.6455 -1.0571 -1.3164 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5633 0.4020 -1.9047 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9690 1.4035 -0.5005 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8404 -0.4312 1.0437 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4841 -1.5842 -0.2888 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7862 0.7857 0.5665 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8963 -2.7017 2.6564 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3250 -2.4298 3.7029 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7863 -1.5829 4.0743 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6945 -1.2038 -1.7904 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6226 -0.2666 -2.3960 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8562 1.2568 0.3385 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1772 1.8783 -1.1614 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5820 0.1780 -1.1326 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0652 -0.5865 0.3385 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7651 2.3983 0.1703 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0775 1.5474 1.5758 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0351 0.0767 1.7268 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5051 1.7901 1.8195 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1858 1.7619 -0.5279 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7295 -0.0202 -0.6486 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3385 -0.5549 1.1331 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7910 1.1574 1.2946 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3949 1.0997 -1.1907 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9889 -0.6625 -1.1724 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3327 -2.2880 -0.0450 H 0 0 0 0 0 0 0 0 0 0 0 0 8.3247 -3.8746 0.1606 H 0 0 0 0 0 0 0 0 0 0 0 0 10.2097 -1.1370 1.2925 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4305 1.8266 0.0786 H 0 0 0 0 0 0 0 0 0 0 0 0 9.6559 2.3491 1.3351 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 2 0 8 10 1 0 6 11 1 0 11 12 2 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 1 0 20 21 2 0 21 22 1 0 22 23 1 0 22 24 2 0 24 25 1 0 25 26 2 0 25 27 1 0 26 20 1 0 1 28 1 0 1 29 1 0 1 30 1 0 2 31 1 0 2 32 1 0 3 33 1 0 3 34 1 0 4 35 1 0 4 36 1 0 5 37 1 0 5 38 1 0 6 39 1 1 10 40 1 0 10 41 1 0 10 42 1 0 11 43 1 0 12 44 1 0 13 45 1 0 13 46 1 0 14 47 1 0 14 48 1 0 15 49 1 0 15 50 1 0 16 51 1 0 16 52 1 0 17 53 1 0 17 54 1 0 18 55 1 0 18 56 1 0 19 57 1 0 19 58 1 0 21 59 1 0 23 60 1 0 24 61 1 0 26 62 1 0 27 63 1 0 M END

Standard InCHIKey	OXFASGUJQBAINI-MGYADMTCSA-N
Standard InCHI	InChI=1S/C23H36O4/c1-3-4-10-14-23(27-19(2)24)15-12-9-7-5-6-8-11-13-20-16-21(25)18-22(26)17-20/h12,15-18,23,25-26H,3-11,13-14H2,1-2H3/b15-12-/t23-/m1/s1
SMILES	CCCCC[C@@H](OC(=O)C)/C=CCCCCCCCc1cc(O)cc(c1)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	376.26	Volume:	419.786 ? Van der Waals volume.
Dense:	0.896	LogP:	6.847 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	4.19 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.874 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	15.0	Rigid Bonds:	8.0
TPSA:	66.76 ? Topological Polar Surface Area.	H-Bond Acceptor:	4.0
H-Bond Donor:	2.0	Rings:	1.0
Heavy Atoms:	4.0

MedChem Properties

QED Drug-Likeness Score:	0.236	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.04	Fsp³:	0.609
MCE-18:	16.0 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted	GSK Rule:	Accepted
Golden Triangle Rule:	Rejected	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.759	Fluc inhibitor:	0.216 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.003 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.074 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.749	Promiscuous compounds:	0.24

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.228	MDCK Permeability:	-4.703
Pgp-inhibitor:	0.608	Pgp-substrate:	0.1
PAMPA:	0.003 ? 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):	0.002
20% Bioavailability (F20%):	0.898	30% Bioavailability (F30%):	0.987
50% Bioavailability (F50%):	0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.002	MRP1:	0.508
Plasma Protein Binding (PPB):	98.031%	Volume Distribution (VD):	0.183
Fu:	1.469% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.858
OATP1B3 inhibitor:	0.934	BCRP inhibitor:	0.744
BSEP inhibitor:	0.946

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	1.0
CYP2C19-inhibitor:	0.03	CYP2C19-substrate:	0.969
CYP2C9-inhibitor:	0.005	CYP2C9-substrate:	0.988
CYP2D6-inhibitor:	0.001	CYP2D6-substrate:	1.0
CYP3A4-inhibitor:	0.104	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.9 ? 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):

4.221

Half-life (T1/2):

0.892

ADMET: Toxicity

hERG Blockers:	0.514	hERG Blockers (10um):	0.771
Human Hepatotoxicity (H-HT):	0.502	Drug-induced Liver Injury (DILI):	0.014
AMES Toxicity:	0.254	Rat Oral Acute Toxicity:	0.194
Maximum Recommended Daily Dose:	0.519	Skin Sensitization:	0.997
Carcinogencity:	0.126	Eye Corrosion:	0.952
Eye Irritation:	0.996	Respiratory Toxicity:	0.654
Drug-induced Neurotoxicity:	0.062	Ototoxicity:	0.16
Hematotoxicity:	0.039	Drug-induced Nephrotoxicity:	0.23
Genotoxicity:	0.001	RPMI-8226 Immunitoxicity:	0.066
A549 Cytotoxicity:	0.883	Hek293 Cytotoxicity:	0.727
BCF:	1.733 ? 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:	5.128 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.233 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	5.641 ? 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
NPO21579	Ononis speciosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8277313]
NPO21579	Ononis speciosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO21579	Ononis speciosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

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
IZ	7

Activity Type	# Activity
Organism	7

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
NPT4085	Organism	Bacillus licheniformis	Bacillus licheniformis	IZ	=	9.0	mm	PMID[16499327]
NPT4085	Organism	Bacillus licheniformis	Bacillus licheniformis	IZ	=	7.0	mm	PMID[19232492]
NPT729	Organism	Micrococcus luteus	Micrococcus luteus	IZ	=	7.0	mm	PMID[23911853]
NPT175	Organism	Enterococcus faecalis	Enterococcus faecalis	IZ	=	6.0	mm	PMID[11000036]
NPT175	Organism	Enterococcus faecalis	Enterococcus faecalis	IZ	=	7.0	mm	PMID[26083682]
NPT4084	Organism	Bacillus circulans	Bacillus circulans	IZ	=	7.0	mm	PMID[20923180]

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 NPC123559 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	10402
0.1-0.2	35968
0.2-0.3	3200
0.3-0.4	195
0.4-0.5	50
0.5-0.6	20
0.6-0.7	18
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	Natural Product ID
0.6667	Remote Similarity	NPC146798
0.6667	Remote Similarity	NPC222522
0.6667	Remote Similarity	NPC106396
0.6667	Remote Similarity	NPC71256
0.6667	Remote Similarity	NPC94351
0.6667	Remote Similarity	NPC168303
0.6458	Remote Similarity	NPC53051
0.6458	Remote Similarity	NPC24404
0.6458	Remote Similarity	NPC313030
0.6275	Remote Similarity	NPC71002
0.6275	Remote Similarity	NPC249828
0.6122	Remote Similarity	NPC39664
0.6042	Remote Similarity	NPC470700
0.6042	Remote Similarity	NPC54844
0.6042	Remote Similarity	NPC39097
0.6042	Remote Similarity	NPC302681
0.6042	Remote Similarity	NPC118286
0.6042	Remote Similarity	NPC109691
0.5962	Remote Similarity	NPC302219
0.5769	Remote Similarity	NPC166761
0.5745	Remote Similarity	NPC294186
0.5745	Remote Similarity	NPC147310
0.5745	Remote Similarity	NPC137415
0.5745	Remote Similarity	NPC166313
0.5745	Remote Similarity	NPC192032
0.5745	Remote Similarity	NPC24407
0.5745	Remote Similarity	NPC11280
0.566	Remote Similarity	NPC242342
0.566	Remote Similarity	NPC85479
0.5517	Remote Similarity	NPC305603
0.541	Remote Similarity	NPC140521
0.537	Remote Similarity	NPC10588
0.537	Remote Similarity	NPC284011
0.5273	Remote Similarity	NPC72947
0.5106	Remote Similarity	NPC246056
0.5091	Remote Similarity	NPC94139
0.5091	Remote Similarity	NPC147284
0.5085	Remote Similarity	NPC486909

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC123559 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4071
0.1-0.2	4947
0.2-0.3	126
0.3-0.4	6
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