NPASS Compound

Natural Product: NPC142087

Natural Product ID	NPC142087
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	(S)-Sargachromenol
IUPAC Name	(2Z,6E)-9-[(2S)-6-hydroxy-2,8-dimethylchromen-2-yl]-6-methyl-2-(4-methylpent-3-enyl)nona-2,6-dienoic acid
Synonyms	(S)-Sargachromenol
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL1668778
PubChem CID	51003425
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001534] Quinone and hydroquinone lipids [CHEMONTID:0001546] Vitamin E compounds [CHEMONTID:0002092] Tocotrienols

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 67 68 0 0 0 0 0 0 0 0999 V2000 -0.7270 0.5019 -3.6601 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2562 0.5307 -2.2865 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9497 1.3254 -1.4371 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1219 2.1280 -1.8520 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3639 1.9546 -1.0889 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9871 0.5840 -1.0436 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.3251 0.0913 -2.4478 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2054 -0.4351 -0.3658 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6439 -1.0712 0.6988 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9422 -0.8235 1.2997 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7189 0.1339 0.6883 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2311 0.7618 -0.4034 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.9736 0.4007 1.2369 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7993 1.4387 0.5629 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.3868 -0.2836 2.3446 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5993 -1.2314 2.9369 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3616 -1.5018 2.4044 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0325 -1.9155 4.0581 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8780 -0.1962 -1.7084 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2059 0.1208 -2.3357 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3206 -0.6124 -1.7462 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2905 -0.0497 -1.0654 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3903 1.3469 -0.8033 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5513 2.1748 -1.1733 O 0 0 0 0 0 0 0 0 0 0 0 0 5.4647 1.8642 -0.1026 O 0 0 0 0 0 0 0 0 0 0 0 0 5.4124 -0.9257 -0.5255 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4387 -0.8663 0.9550 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5391 -1.7338 1.4794 C 0 0 0 0 0 0 0 0 0 0 0 0 7.5318 -1.2666 2.2069 C 0 0 0 0 0 0 0 0 0 0 0 0 8.5879 -2.1725 2.6952 C 0 0 0 0 0 0 0 0 0 0 0 0 7.5847 0.1729 2.5338 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6772 1.5594 -4.0569 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1180 -0.0895 -4.3627 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7695 0.1925 -3.8003 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6566 1.4008 -0.3881 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3231 2.0279 -2.9475 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7992 3.2075 -1.6978 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2873 2.3156 -0.0403 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1341 2.6255 -1.5533 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3445 -0.3314 -2.4260 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2260 0.9408 -3.1503 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6645 -0.7659 -2.7174 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2118 -0.7334 -0.7053 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0242 -1.8318 1.1813 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.6841 2.3728 1.1337 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.8499 1.0556 0.5840 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.4543 1.6154 -0.4647 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.3731 -0.0519 2.7495 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7317 -2.2457 2.8612 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.9413 -2.3283 4.1021 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9792 -0.0562 -0.6139 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6629 -1.2867 -1.8415 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4272 1.1302 -2.5771 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1037 -0.3663 -3.3962 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4032 -1.7194 -1.8486 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6161 2.8564 0.0267 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2854 -1.9228 -0.9270 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3494 -0.4959 -0.9844 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5829 0.1579 1.3199 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4857 -1.2621 1.3949 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4832 -2.7769 1.2313 H 0 0 0 0 0 0 0 0 0 0 0 0 8.0927 -3.0994 3.1040 H 0 0 0 0 0 0 0 0 0 0 0 0 9.3041 -2.4876 1.9119 H 0 0 0 0 0 0 0 0 0 0 0 0 9.1265 -1.7371 3.5724 H 0 0 0 0 0 0 0 0 0 0 0 0 7.6226 0.7450 1.5704 H 0 0 0 0 0 0 0 0 0 0 0 0 8.4783 0.3987 3.1646 H 0 0 0 0 0 0 0 0 0 0 0 0 6.6969 0.5409 3.0776 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 0 3 4 1 0 4 5 1 0 6 5 1 6 6 7 1 0 6 8 1 0 8 9 2 0 9 10 1 0 10 11 2 0 11 12 1 0 11 13 1 0 13 14 1 0 13 15 2 0 15 16 1 0 16 17 2 0 16 18 1 0 2 19 1 0 19 20 1 0 20 21 1 0 21 22 2 0 22 23 1 0 23 24 2 0 23 25 1 0 22 26 1 0 26 27 1 0 27 28 1 0 28 29 2 3 29 30 1 0 29 31 1 0 12 6 1 0 17 10 1 0 1 32 1 0 1 33 1 0 1 34 1 0 3 35 1 0 4 36 1 0 4 37 1 0 5 38 1 0 5 39 1 0 7 40 1 0 7 41 1 0 7 42 1 0 8 43 1 0 9 44 1 0 14 45 1 0 14 46 1 0 14 47 1 0 15 48 1 0 17 49 1 0 18 50 1 0 19 51 1 0 19 52 1 0 20 53 1 0 20 54 1 0 21 55 1 0 25 56 1 0 26 57 1 0 26 58 1 0 27 59 1 0 27 60 1 0 28 61 1 0 30 62 1 0 30 63 1 0 30 64 1 0 31 65 1 0 31 66 1 0 31 67 1 0 M END

Standard InCHIKey	QKXAGRZCXAYBQX-UATDQJHISA-N
Standard InCHI	InChI=1S/C27H36O4/c1-19(2)9-6-12-22(26(29)30)13-7-10-20(3)11-8-15-27(5)16-14-23-18-24(28)17-21(4)25(23)31-27/h9,11,13-14,16-18,28H,6-8,10,12,15H2,1-5H3,(H,29,30)/b20-11+,22-13-/t27-/m0/s1
SMILES	C/C(=CCC[C@@]1(C)C=Cc2c(O1)c(C)cc(c2)O)/CC/C=C(C(=O)O)/CCC=C(C)C

Calculated Properties

Physi-Chem Properties

Molecular Weight:	424.26	Volume:	472.504 ? Van der Waals volume.
Dense:	0.898	LogP:	6.997 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.642 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.752 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	10.0	Rigid Bonds:	15.0
TPSA:	66.76 ? Topological Polar Surface Area.	H-Bond Acceptor:	4.0
H-Bond Donor:	2.0	Rings:	2.0
Heavy Atoms:	4.0

MedChem Properties

QED Drug-Likeness Score:	0.31	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.832	Fsp³:	0.444
MCE-18:	51.872 ? 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:	0.931	Fluc inhibitor:	0.127 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.137 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.644 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.561	Promiscuous compounds:	0.055

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.843	MDCK Permeability:	-4.781
Pgp-inhibitor:	0.375	Pgp-substrate:	0.0
PAMPA:	0.372 ? 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):	0.015
20% Bioavailability (F20%):	0.489	30% Bioavailability (F30%):	0.369
50% Bioavailability (F50%):	0.942

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.997
Plasma Protein Binding (PPB):	95.566%	Volume Distribution (VD):	-0.546
Fu:	5.064% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	0.905	BCRP inhibitor:	0.0
BSEP inhibitor:	0.988

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.305
CYP2C19-inhibitor:	0.071	CYP2C19-substrate:	0.141
CYP2C9-inhibitor:	0.918	CYP2C9-substrate:	0.001
CYP2D6-inhibitor:	0.001	CYP2D6-substrate:	0.005
CYP3A4-inhibitor:	0.007	CYP3A4-substrate:	0.998
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.524 ? 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):

5.304

Half-life (T1/2):

0.812

ADMET: Toxicity

hERG Blockers:	0.143	hERG Blockers (10um):	0.341
Human Hepatotoxicity (H-HT):	0.746	Drug-induced Liver Injury (DILI):	0.141
AMES Toxicity:	0.115	Rat Oral Acute Toxicity:	0.226
Maximum Recommended Daily Dose:	0.279	Skin Sensitization:	0.984
Carcinogencity:	0.229	Eye Corrosion:	0.014
Eye Irritation:	0.891	Respiratory Toxicity:	0.73
Drug-induced Neurotoxicity:	0.332	Ototoxicity:	0.545
Hematotoxicity:	0.2	Drug-induced Nephrotoxicity:	0.632
Genotoxicity:	0.183	RPMI-8226 Immunitoxicity:	0.048
A549 Cytotoxicity:	0.104	Hek293 Cytotoxicity:	0.16
BCF:	2.041 ? 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:	5.189 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.51 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	5.996 ? 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
NPO21423	Botryllus tuberatus	Species	Styelidae	Eukaryota	n.a.	n.a.	n.a.	PMID[21142112]
NPO21423	Botryllus tuberatus	Species	Styelidae	Eukaryota	n.a.	Korean	n.a.	PMID[21142112]
NPO21423	Botryllus tuberatus	Species	Styelidae	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
IC50	1

Activity Type	# Activity
Individual protein	1

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT540	Individual protein	Bile acid receptor FXR	Homo sapiens	IC50	=	17000.0	nM	PubChem BioAssay data set

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 NPC142087 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	14578
0.1-0.2	33137
0.2-0.3	1910
0.3-0.4	158
0.4-0.5	62
0.5-0.6	10
0.6-0.7	1
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC95034
0.6774	Remote Similarity	NPC473718
0.5714	Remote Similarity	NPC185634
0.5556	Remote Similarity	NPC317601
0.5556	Remote Similarity	NPC329427
0.5395	Remote Similarity	NPC114918
0.5395	Remote Similarity	NPC483462
0.5385	Remote Similarity	NPC479050
0.5342	Remote Similarity	NPC74137
0.5309	Remote Similarity	NPC474237
0.527	Remote Similarity	NPC608493
0.5195	Remote Similarity	NPC483463

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC142087 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3966
0.1-0.2	5118
0.2-0.3	65
0.3-0.4	0
0.4-0.5	1
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