NPASS Compound

Natural Product: NPC181094

Natural Product ID	NPC181094
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	DVWSXZIHSUZZKJ-UHFFFAOYSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	9316
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0003909] Fatty Acyls [CHEMONTID:0000504] Lineolic acids and derivatives

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 53 52 0 0 0 0 0 0 0 0999 V2000 -5.1629 1.6765 -2.7856 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2087 1.0947 -1.8688 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9630 -0.3562 -1.6928 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7279 -0.8625 -0.4894 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4833 -2.2727 -0.2742 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2263 -2.7412 0.2658 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1619 -2.1180 0.5802 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8793 -0.6737 0.4773 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6057 -0.0783 1.7955 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5191 0.5174 2.1343 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3460 0.7173 1.2698 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8161 0.0108 1.9624 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0917 0.1704 1.1213 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2087 -0.5328 1.8294 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4814 -0.4265 1.0340 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8484 1.0254 0.8719 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1176 1.2667 0.1216 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0482 0.7517 -1.2623 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0373 0.2301 -1.7497 O 0 0 0 0 0 0 0 0 0 0 0 0 7.1850 0.8569 -2.0713 O 0 0 0 0 0 0 0 0 0 0 0 0 7.1107 0.3634 -3.3894 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1567 1.5932 -2.2989 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1482 1.0949 -3.7471 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3610 2.7436 -2.9341 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1270 1.5919 -0.9015 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.2156 1.2914 -2.2956 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9645 -1.0594 -2.5304 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7583 -0.1636 0.3745 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5996 -2.7826 -1.2868 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2972 -2.7010 0.3924 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1656 -3.8735 0.4478 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2790 -2.7006 1.0018 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5713 -0.0534 -0.0668 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9400 -0.6440 -0.1777 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4254 -0.1668 2.5392 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4512 0.9181 3.1632 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1223 1.8238 1.2122 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4162 0.3952 0.2352 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9440 0.4715 2.9497 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5661 -1.0517 2.1059 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9468 -0.2289 0.1160 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2289 1.2712 1.0547 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4126 -0.0097 2.8010 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9535 -1.5805 2.0807 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3152 -0.9993 1.5198 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2627 -0.9138 0.0482 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0314 1.5351 0.3128 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9301 1.5295 1.8500 H 0 0 0 0 0 0 0 0 0 0 0 0 7.0073 0.8436 0.6399 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3293 2.3583 0.0394 H 0 0 0 0 0 0 0 0 0 0 0 0 8.0460 -0.2143 -3.5997 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1964 -0.1941 -3.5993 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1676 1.2567 -4.0643 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 2 3 4 5 1 0 5 6 1 0 6 7 2 3 7 8 1 0 8 9 1 0 9 10 2 3 10 11 1 0 11 12 1 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 2 0 18 20 1 0 20 21 1 0 1 22 1 0 1 23 1 0 1 24 1 0 2 25 1 0 2 26 1 0 3 27 1 0 4 28 1 0 5 29 1 0 5 30 1 0 6 31 1 0 7 32 1 0 8 33 1 0 8 34 1 0 9 35 1 0 10 36 1 0 11 37 1 0 11 38 1 0 12 39 1 0 12 40 1 0 13 41 1 0 13 42 1 0 14 43 1 0 14 44 1 0 15 45 1 0 15 46 1 0 16 47 1 0 16 48 1 0 17 49 1 0 17 50 1 0 21 51 1 0 21 52 1 0 21 53 1 0 M END

Standard InCHIKey	DVWSXZIHSUZZKJ-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C19H32O2/c1-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19(20)21-2/h4-5,7-8,10-11H,3,6,9,12-18H2,1-2H3
SMILES	CCC=CCC=CCC=CCCCCCCCC(=O)OC

Calculated Properties

Physi-Chem Properties

Molecular Weight:	292.24	Volume:	344.215 ? Van der Waals volume.
Dense:	0.849	LogP:	6.281 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.821 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-5.882 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	14.0	Rigid Bonds:	4.0
TPSA:	26.3 ? Topological Polar Surface Area.	H-Bond Acceptor:	2.0
H-Bond Donor:	0.0	Rings:	0.0
Heavy Atoms:	2.0

MedChem Properties

QED Drug-Likeness Score:	0.245	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	2.595	Fsp³:	0.632
MCE-18:	0.0 ? 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:	0.155	Fluc inhibitor:	0.327 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.004 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.013 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.995	Promiscuous compounds:	0.351

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.974	MDCK Permeability:	-4.744
Pgp-inhibitor:	0.479	Pgp-substrate:	0.035
PAMPA:	0.008 ? 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%):	0.295	30% Bioavailability (F30%):	0.726
50% Bioavailability (F50%):	0.801

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.129	MRP1:	0.987
Plasma Protein Binding (PPB):	97.689%	Volume Distribution (VD):	-0.4
Fu:	2.266% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.147
OATP1B3 inhibitor:	0.903	BCRP inhibitor:	0.507
BSEP inhibitor:	0.985

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.999
CYP2C19-inhibitor:	0.066	CYP2C19-substrate:	0.221
CYP2C9-inhibitor:	1.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	1.0	CYP2D6-substrate:	1.0
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	1.0
CYP2B6-substrate:	1.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.771 ? 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):

6.306

Half-life (T1/2):

0.191

ADMET: Toxicity

hERG Blockers:	0.173	hERG Blockers (10um):	0.457
Human Hepatotoxicity (H-HT):	0.106	Drug-induced Liver Injury (DILI):	0.005
AMES Toxicity:	0.537	Rat Oral Acute Toxicity:	0.107
Maximum Recommended Daily Dose:	0.123	Skin Sensitization:	1.0
Carcinogencity:	0.423	Eye Corrosion:	0.989
Eye Irritation:	0.996	Respiratory Toxicity:	0.826
Drug-induced Neurotoxicity:	0.068	Ototoxicity:	0.189
Hematotoxicity:	0.026	Drug-induced Nephrotoxicity:	0.23
Genotoxicity:	0.0	RPMI-8226 Immunitoxicity:	0.026
A549 Cytotoxicity:	0.025	Hek293 Cytotoxicity:	0.019
BCF:	1.731 ? 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:	4.592 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.975 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.945 ? 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
NPO9445	Crocus sativus	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1002/hlca.19270100148]
NPO9445	Crocus sativus	Species	Iridaceae	Eukaryota	Petals	n.a.	n.a.	PMID[15043425]
NPO9445	Crocus sativus	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24338885]
NPO9445	Crocus sativus	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[37111302]
NPO9445	Crocus sativus	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO9445	Crocus sativus	Species	Iridaceae	Eukaryota	Silk Stigma Style	n.a.	n.a.	Database[FooDB]
NPO9445	Crocus sativus	Species	Iridaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO9445	Crocus sativus	Species	Iridaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO9445	Crocus sativus	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9445	Crocus sativus	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9445	Crocus sativus	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9445	Crocus sativus	Species	Iridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO9445	Crocus sativus	Species	Iridaceae	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

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

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 NPC181094 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	23590
0.1-0.2	24454
0.2-0.3	1471
0.3-0.4	262
0.4-0.5	52
0.5-0.6	18
0.6-0.7	4
0.7-0.8	0
0.8-0.85	0
0.85-0.9	1
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC139545
0.8621	High Similarity	NPC39633
0.7586	Intermediate Similarity	NPC309606
0.75	Intermediate Similarity	NPC10316
0.75	Intermediate Similarity	NPC200845
0.6562	Remote Similarity	NPC228473
0.6471	Remote Similarity	NPC28779
0.6316	Remote Similarity	NPC271921
0.6	Remote Similarity	NPC216130
0.5854	Remote Similarity	NPC473772
0.5641	Remote Similarity	NPC475443
0.5641	Remote Similarity	NPC473829
0.5588	Remote Similarity	NPC128061
0.5556	Remote Similarity	NPC219536
0.5556	Remote Similarity	NPC31551
0.5517	Remote Similarity	NPC201622
0.5517	Remote Similarity	NPC305660
0.5517	Remote Similarity	NPC161097
0.5517	Remote Similarity	NPC28598
0.5517	Remote Similarity	NPC22903
0.5517	Remote Similarity	NPC54980
0.55	Remote Similarity	NPC330426
0.55	Remote Similarity	NPC127091
0.55	Remote Similarity	NPC22101
0.5366	Remote Similarity	NPC54925
0.5185	Remote Similarity	NPC57499
0.5135	Remote Similarity	NPC223677

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC181094 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7101
0.1-0.2	1951
0.2-0.3	77
0.3-0.4	17
0.4-0.5	1
0.5-0.6	1
0.6-0.7	2
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
0.6364	Remote Similarity	NPD5343	Phase 4
0.6	Remote Similarity	NPD6096	Phase 4
0.5294	Remote Similarity	NPD6097	Approved

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