NPASS Compound

Natural Product: NPC129373

Natural Product ID	NPC129373
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	10'(Z)-Heptadecenylhydroquinone
IUPAC Name	2-[(Z)-heptadec-10-enyl]benzene-1,4-diol
Synonyms	10'(Z)-Heptadecenylhydroquinone
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL463915
PubChem CID	10736383
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0000134] Phenols [CHEMONTID:0001286] Benzenediols [CHEMONTID:0000136] Hydroquinones

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 -6.5155 4.2110 -0.9783 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4137 3.7563 -0.0567 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4139 2.2545 0.1473 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2680 1.9348 1.0835 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2563 0.4476 1.2960 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1295 0.0008 2.2386 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8574 0.3965 1.6359 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9177 -0.4560 1.2977 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9998 -1.9060 1.4700 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9063 -2.6832 0.2129 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2563 -2.5642 -0.6833 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6112 -2.9176 -0.2932 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3431 -2.1715 0.7705 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7237 -2.7060 0.9682 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7636 -2.7053 -0.0354 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4032 -1.5264 -0.5622 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9621 -0.4332 -1.3851 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8469 0.4464 -1.0775 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0407 1.4698 -0.1447 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9608 2.2545 0.1663 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1106 3.2820 1.0886 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7130 2.0654 -0.4052 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5226 1.0567 -1.3262 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5939 0.2709 -1.6418 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3729 -0.7342 -2.5825 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.1243 5.0342 -1.6440 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8895 3.4172 -1.6443 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.3806 4.6330 -0.4107 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6116 4.1887 0.9685 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4149 4.1428 -0.3359 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3379 1.7554 -0.8275 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3955 1.9922 0.5812 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3449 2.2138 0.5244 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4235 2.5224 1.9955 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0789 -0.0077 0.2793 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2381 0.0890 1.6300 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2624 -1.0143 2.5562 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2800 0.6310 3.1835 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7151 1.4850 1.4734 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0078 -0.0131 0.8494 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2395 -2.2366 2.1928 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9658 -2.2126 1.9838 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8902 -2.5981 -0.3838 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9540 -3.7964 0.5074 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2261 -1.5038 -1.1549 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0311 -3.1685 -1.6315 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2657 -2.9472 -1.2133 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6245 -4.0187 0.1133 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8588 -2.4090 1.8031 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2450 -1.0808 0.7298 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5746 -3.7853 1.3792 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1232 -2.2081 1.9177 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6351 -3.3415 0.4295 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5049 -3.4482 -0.8970 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8932 -0.9863 0.3935 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4554 -1.8691 -1.0440 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8544 0.3017 -1.5664 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8429 -0.7756 -2.5055 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0201 1.5998 0.2881 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6503 3.2017 1.9376 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9140 2.7149 -0.1151 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5240 0.9351 -1.7589 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8112 -0.4808 -3.3924 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 2 0 8 9 1 0 9 10 1 0 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 19 20 1 0 20 21 1 0 20 22 2 0 22 23 1 0 23 24 2 0 24 25 1 0 24 18 1 0 1 26 1 0 1 27 1 0 1 28 1 0 2 29 1 0 2 30 1 0 3 31 1 0 3 32 1 0 4 33 1 0 4 34 1 0 5 35 1 0 5 36 1 0 6 37 1 0 6 38 1 0 7 39 1 0 8 40 1 0 9 41 1 0 9 42 1 0 10 43 1 0 10 44 1 0 11 45 1 0 11 46 1 0 12 47 1 0 12 48 1 0 13 49 1 0 13 50 1 0 14 51 1 0 14 52 1 0 15 53 1 0 15 54 1 0 16 55 1 0 16 56 1 0 17 57 1 0 17 58 1 0 19 59 1 0 21 60 1 0 22 61 1 0 23 62 1 0 25 63 1 0 M END

Standard InCHIKey	YPWFIMVHFFOLQG-FPLPWBNLSA-N
Standard InCHI	InChI=1S/C23H38O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-21-20-22(24)18-19-23(21)25/h7-8,18-20,24-25H,2-6,9-17H2,1H3/b8-7-
SMILES	CCCCCC/C=CCCCCCCCCCc1cc(O)ccc1O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	346.29	Volume:	404.842 ? Van der Waals volume.
Dense:	0.855	LogP:	8.738 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	4.913 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-6.953 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	15.0	Rigid Bonds:	7.0
TPSA:	40.46 ? Topological Polar Surface Area.	H-Bond Acceptor:	2.0
H-Bond Donor:	2.0	Rings:	1.0
Heavy Atoms:	2.0

MedChem Properties

QED Drug-Likeness Score:	0.199	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	2.28	Fsp³:	0.652
MCE-18:	6.0 ? 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:	1
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.817	Fluc inhibitor:	0.326 ? 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:	0.125 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.952	Promiscuous compounds:	0.156

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.057	MDCK Permeability:	-4.726
Pgp-inhibitor:	0.675	Pgp-substrate:	0.0
PAMPA:	0.0 ? 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):	0.029
20% Bioavailability (F20%):	0.922	30% Bioavailability (F30%):	0.986
50% Bioavailability (F50%):	0.984

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.002	MRP1:	0.968
Plasma Protein Binding (PPB):	98.92%	Volume Distribution (VD):	0.392
Fu:	0.247% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.414
OATP1B3 inhibitor:	0.999	BCRP inhibitor:	0.877
BSEP inhibitor:	1.0

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	1.0
CYP2C19-inhibitor:	0.002	CYP2C19-substrate:	0.455
CYP2C9-inhibitor:	0.999	CYP2C9-substrate:	0.838
CYP2D6-inhibitor:	0.999	CYP2D6-substrate:	0.804
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.002	CYP2C8-inhibitor:	1.0
HLM stability:	0.102 ? 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):

5.755

Half-life (T1/2):

0.511

ADMET: Toxicity

hERG Blockers:	0.482	hERG Blockers (10um):	0.885
Human Hepatotoxicity (H-HT):	0.252	Drug-induced Liver Injury (DILI):	0.002
AMES Toxicity:	0.141	Rat Oral Acute Toxicity:	0.162
Maximum Recommended Daily Dose:	0.371	Skin Sensitization:	1.0
Carcinogencity:	0.071	Eye Corrosion:	0.99
Eye Irritation:	0.996	Respiratory Toxicity:	0.905
Drug-induced Neurotoxicity:	0.007	Ototoxicity:	0.133
Hematotoxicity:	0.013	Drug-induced Nephrotoxicity:	0.285
Genotoxicity:	0.0	RPMI-8226 Immunitoxicity:	0.1
A549 Cytotoxicity:	0.972	Hek293 Cytotoxicity:	0.762
BCF:	1.782 ? 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:	5.879 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.487 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	6.433 ? 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
NPO33250	rhus succedanea	Species	Anacardiaceae	Eukaryota	sap	n.a.	n.a.	PMID[12444713]
NPO33250	rhus succedanea	Species	Anacardiaceae	Eukaryota	seed kernels	Fukuoka, Japan	n.a.	PMID[9322359]
NPO12586	Tapirira guianensis	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9514013]
NPO12586	Tapirira guianensis	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO12586	Tapirira guianensis	Species	Anacardiaceae	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	12

Activity Type	# Activity
Cell line	9
Non-molecular	3

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
NPT165	Cell line	HeLa	Homo sapiens	IC50	=	4.7	ug.mL-1	PMID[17958396]
NPT1229	Cell line	Huh-7	Homo sapiens	IC50	=	6.4	ug.mL-1	PMID[17958396]
NPT393	Cell line	HCT-116	Homo sapiens	IC50	=	3.4	ug.mL-1	PMID[17958396]
NPT114	Cell line	LoVo	Homo sapiens	IC50	=	2.9	ug.mL-1	PMID[19467877]
NPT76	Cell line	C6	Rattus norvegicus	IC50	=	1.1	ug.mL-1	PMID[17958396]
NPT1034	Cell line	Lu1	Homo sapiens	IC50	=	0.3	ug.mL-1	PMID[22617493]
NPT1851	Cell line	Col2	Homo sapiens	IC50	=	0.8	ug.mL-1	PMID[22617493]
NPT91	Cell line	KB	Homo sapiens	IC50	=	0.5	ug.mL-1	PMID[11325248]
NPT858	Cell line	LNCaP	Homo sapiens	IC50	=	0.2	ug.mL-1	PMID[12141856]
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	IC50	=	1.3	ug.mL-1	PMID[9514013]
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	IC50	=	0.5	ug.mL-1	PMID[9514013]
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	IC50	=	0.6	ug.mL-1	PMID[9514013]

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 NPC129373 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	27428
0.1-0.2	19973
0.2-0.3	2191
0.3-0.4	156
0.4-0.5	66
0.5-0.6	23
0.6-0.7	11
0.7-0.8	0
0.8-0.85	0
0.85-0.9	1
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.875	High Similarity	NPC48730
0.7727	Intermediate Similarity	NPC248396
0.6818	Remote Similarity	NPC481193
0.6818	Remote Similarity	NPC481192
0.6364	Remote Similarity	NPC94139
0.6364	Remote Similarity	NPC147284
0.6136	Remote Similarity	NPC483454
0.6136	Remote Similarity	NPC162314
0.6047	Remote Similarity	NPC146798
0.6047	Remote Similarity	NPC222522
0.6047	Remote Similarity	NPC106396
0.6047	Remote Similarity	NPC94351
0.6047	Remote Similarity	NPC168303
0.5909	Remote Similarity	NPC232523
0.5814	Remote Similarity	NPC53051
0.5814	Remote Similarity	NPC24404
0.5814	Remote Similarity	NPC313030
0.5652	Remote Similarity	NPC71002
0.5652	Remote Similarity	NPC249828
0.5625	Remote Similarity	NPC210497
0.5435	Remote Similarity	NPC488413
0.5435	Remote Similarity	NPC488412
0.5349	Remote Similarity	NPC470700
0.5349	Remote Similarity	NPC54844
0.5349	Remote Similarity	NPC39097
0.5349	Remote Similarity	NPC302681
0.5349	Remote Similarity	NPC118286
0.5349	Remote Similarity	NPC109691
0.5333	Remote Similarity	NPC55561
0.5319	Remote Similarity	NPC302219
0.5217	Remote Similarity	NPC196479
0.5217	Remote Similarity	NPC487734
0.5208	Remote Similarity	NPC158253
0.52	Remote Similarity	NPC483450
0.5111	Remote Similarity	NPC39664
0.5111	Remote Similarity	NPC177420

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC129373 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6519
0.1-0.2	2485
0.2-0.3	139
0.3-0.4	5
0.4-0.5	1
0.5-0.6	1
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
0.5116	Remote Similarity	NPD846	Phase 4

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