NPASS Compound

Natural Product: NPC284011

Natural Product ID	NPC284011
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	5-Heptadeca-9'e,11'z,16-Trienylresorcinol
IUPAC Name	5-[(9E,11Z)-heptadeca-9,11,16-trienyl]benzene-1,3-diol
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL443135
PubChem CID	11695842
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0000134] Phenols [CHEMONTID:0001286] Benzenediols [CHEMONTID:0000137] Resorcinols

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 59 59 0 0 0 0 0 0 0 0999 V2000 8.8847 -2.0894 -0.6676 C 0 0 0 0 0 0 0 0 0 0 0 0 8.9494 -0.9958 0.0655 C 0 0 0 0 0 0 0 0 0 0 0 0 8.0439 -0.7997 1.1929 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1749 0.4273 1.0623 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3001 0.3755 -0.1734 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4221 -0.8019 -0.1009 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1311 -0.7073 -0.1045 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3844 0.5064 -0.1766 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0611 0.4950 -0.1736 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3266 1.7608 -0.2489 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4317 1.9878 0.9515 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6013 0.9147 1.1096 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5231 0.7985 -0.0768 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2364 2.1122 -0.2563 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1711 2.0181 -1.4441 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2029 0.9427 -1.2608 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0715 1.1570 -0.0597 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0422 0.0045 -0.0191 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.2594 0.0815 -0.6611 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.1204 -0.9921 -0.6017 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.3320 -0.8896 -1.2525 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.8107 -2.1644 0.0863 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5989 -2.2318 0.7212 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.7418 -1.1550 0.6584 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2787 -3.3913 1.4086 O 0 0 0 0 0 0 0 0 0 0 0 0 9.5497 -2.2487 -1.5067 H 0 0 0 0 0 0 0 0 0 0 0 0 8.1546 -2.8487 -0.4325 H 0 0 0 0 0 0 0 0 0 0 0 0 9.6876 -0.2502 -0.1885 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3809 -1.6755 1.3092 H 0 0 0 0 0 0 0 0 0 0 0 0 8.6675 -0.7328 2.1218 H 0 0 0 0 0 0 0 0 0 0 0 0 7.8566 1.2997 0.9675 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5315 0.5876 1.9397 H 0 0 0 0 0 0 0 0 0 0 0 0 6.9242 0.3759 -1.0992 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7256 1.3036 -0.2076 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8759 -1.8107 -0.0425 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5644 -1.6562 -0.0461 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8542 1.4677 -0.2360 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5424 -0.4423 -0.1159 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7202 1.7440 -1.1886 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0134 2.6075 -0.3434 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0183 3.0109 0.8605 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0701 1.9603 1.8602 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2400 1.2069 1.9784 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0661 -0.0310 1.3242 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2614 -0.0057 0.1115 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9158 0.5503 -0.9568 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8114 2.3994 0.6224 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4835 2.9072 -0.5057 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5772 1.7383 -2.3550 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6185 3.0034 -1.6798 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7518 -0.0491 -1.2784 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8833 1.0103 -2.1599 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4864 1.2128 0.8720 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6268 2.1149 -0.1572 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.5072 0.9947 -1.2002 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.7746 -0.0010 -1.3351 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.4955 -3.0018 0.1260 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7746 -1.2093 1.1654 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9823 -4.0056 1.7977 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 2 3 1 0 3 4 1 0 4 5 1 0 5 6 1 0 6 7 2 0 7 8 1 0 8 9 2 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 23 25 1 0 24 18 1 0 1 26 1 0 1 27 1 0 2 28 1 0 3 29 1 0 3 30 1 0 4 31 1 0 4 32 1 0 5 33 1 0 5 34 1 0 6 35 1 0 7 36 1 0 8 37 1 0 9 38 1 0 10 39 1 0 10 40 1 0 11 41 1 0 11 42 1 0 12 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 19 55 1 0 21 56 1 0 22 57 1 0 24 58 1 0 25 59 1 0 M END

Standard InCHIKey	CRWZHBSCOWOZJQ-NMMTYZSQSA-N
Standard InCHI	InChI=1S/C23H34O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-21-18-22(24)20-23(25)19-21/h2,6-9,18-20,24-25H,1,3-5,10-17H2/b7-6-,9-8+
SMILES	C=CCCC/C=CC=CCCCCCCCCc1cc(O)cc(c1)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	342.26	Volume:	399.569 ? Van der Waals volume.
Dense:	0.857	LogP:	7.368 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	4.346 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-5.213 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	14.0	Rigid Bonds:	9.0
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:	0.221	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	2.718	Fsp³:	0.478
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:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.675	Fluc inhibitor:	0.713 ? 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:	0.272 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.869	Promiscuous compounds:	0.104

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.189	MDCK Permeability:	-4.74
Pgp-inhibitor:	0.704	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):	0.0
20% Bioavailability (F20%):	0.869	30% Bioavailability (F30%):	0.991
50% Bioavailability (F50%):	0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.037
Plasma Protein Binding (PPB):	98.823%	Volume Distribution (VD):	-0.27
Fu:	0.574% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.961
OATP1B3 inhibitor:	0.996	BCRP inhibitor:	0.936
BSEP inhibitor:	1.0

ADMET: Metabolism

CYP1A2-inhibitor:	0.398	CYP1A2-substrate:	1.0
CYP2C19-inhibitor:	0.019	CYP2C19-substrate:	0.996
CYP2C9-inhibitor:	1.0	CYP2C9-substrate:	1.0
CYP2D6-inhibitor:	0.985	CYP2D6-substrate:	0.999
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.982 ? 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):

5.193

Half-life (T1/2):

0.829

ADMET: Toxicity

hERG Blockers:	0.639	hERG Blockers (10um):	0.864
Human Hepatotoxicity (H-HT):	0.457	Drug-induced Liver Injury (DILI):	0.004
AMES Toxicity:	0.365	Rat Oral Acute Toxicity:	0.12
Maximum Recommended Daily Dose:	0.88	Skin Sensitization:	1.0
Carcinogencity:	0.091	Eye Corrosion:	0.528
Eye Irritation:	0.988	Respiratory Toxicity:	0.586
Drug-induced Neurotoxicity:	0.078	Ototoxicity:	0.254
Hematotoxicity:	0.018	Drug-induced Nephrotoxicity:	0.079
Genotoxicity:	0.001	RPMI-8226 Immunitoxicity:	0.057
A549 Cytotoxicity:	0.858	Hek293 Cytotoxicity:	0.891
BCF:	1.843 ? 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:	5.095 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.255 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	5.913 ? 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
NPO25294	Merulius incarnatus	Species	Meruliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16643059]
NPO25294	Merulius incarnatus	Species	Meruliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO25294	Merulius incarnatus	Species	Meruliaceae	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
Organism	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
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	IC50	=	15.0	ug.mL-1	DrugMatrix in vivo data: Hematology

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 NPC284011 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	31445
0.1-0.2	17262
0.2-0.3	974
0.3-0.4	87
0.4-0.5	36
0.5-0.6	22
0.6-0.7	13
0.7-0.8	0
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.825	Intermediate Similarity	NPC72947
0.7838	Intermediate Similarity	NPC470700
0.7838	Intermediate Similarity	NPC54844
0.7838	Intermediate Similarity	NPC39097
0.7838	Intermediate Similarity	NPC302681
0.7838	Intermediate Similarity	NPC118286
0.7838	Intermediate Similarity	NPC109691
0.7561	Intermediate Similarity	NPC10588
0.7436	Intermediate Similarity	NPC53051
0.7436	Intermediate Similarity	NPC24404
0.7436	Intermediate Similarity	NPC313030
0.7436	Intermediate Similarity	NPC39664
0.725	Intermediate Similarity	NPC146798
0.725	Intermediate Similarity	NPC222522
0.725	Intermediate Similarity	NPC106396
0.725	Intermediate Similarity	NPC94351
0.725	Intermediate Similarity	NPC168303
0.6744	Remote Similarity	NPC71002
0.6744	Remote Similarity	NPC302219
0.6744	Remote Similarity	NPC242342
0.6744	Remote Similarity	NPC249828
0.6744	Remote Similarity	NPC85479
0.6667	Remote Similarity	NPC246056
0.6154	Remote Similarity	NPC294186
0.6154	Remote Similarity	NPC147310
0.6154	Remote Similarity	NPC137415
0.6154	Remote Similarity	NPC166313
0.6154	Remote Similarity	NPC192032
0.6154	Remote Similarity	NPC24407
0.6154	Remote Similarity	NPC11280
0.58	Remote Similarity	NPC305603
0.58	Remote Similarity	NPC61033
0.58	Remote Similarity	NPC127894
0.58	Remote Similarity	NPC470759
0.5778	Remote Similarity	NPC166761
0.5714	Remote Similarity	NPC241891
0.5714	Remote Similarity	NPC134829
0.5625	Remote Similarity	NPC192
0.5581	Remote Similarity	NPC487946
0.5581	Remote Similarity	NPC487945
0.5532	Remote Similarity	NPC204901
0.5435	Remote Similarity	NPC483454
0.5435	Remote Similarity	NPC162314
0.54	Remote Similarity	NPC470760
0.537	Remote Similarity	NPC123559
0.537	Remote Similarity	NPC140521
0.5319	Remote Similarity	NPC94139
0.5319	Remote Similarity	NPC147284
0.5217	Remote Similarity	NPC232523
0.5217	Remote Similarity	NPC486908
0.5106	Remote Similarity	NPC488413
0.5106	Remote Similarity	NPC488412

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC284011 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7138
0.1-0.2	1957
0.2-0.3	51
0.3-0.4	4
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