NPASS Compound

Natural Product: NPC72947

Natural Product ID	NPC72947
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	5-Heptadeca-8'z,11'z,16-Trienylresorcinol
IUPAC Name	5-[(8Z,11Z)-heptadeca-8,11,16-trienyl]benzene-1,3-diol
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL496449
PubChem CID	11573713
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 4.5369 -0.6313 -3.9400 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6259 -1.1919 -2.7498 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9061 -1.3242 -2.0610 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9548 -0.6189 -0.7283 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8958 -1.1673 0.2246 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0167 -0.4375 1.4660 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0563 0.2845 1.9687 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7640 0.4094 1.2956 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5610 1.8544 1.0138 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5376 2.4952 1.5132 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4700 1.9658 2.3807 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8408 2.1713 1.6294 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9732 1.6742 2.4814 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8433 0.2371 2.7799 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7437 -0.7669 1.7270 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8488 -0.9749 0.7779 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1607 0.1682 -0.1094 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2902 -0.2956 -1.0074 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5716 -0.0864 -0.5693 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6230 -0.5095 -1.3880 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.9358 -0.3128 -0.9741 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.3131 -1.1126 -2.5885 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0020 -1.3096 -3.0030 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9538 -0.8916 -2.1943 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7072 -1.9125 -4.2030 O 0 0 0 0 0 0 0 0 0 0 0 0 5.4470 -0.2658 -4.4020 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6009 -0.5167 -4.4806 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7209 -1.5540 -2.2931 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7201 -0.8933 -2.6796 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1369 -2.4030 -1.9261 H 0 0 0 0 0 0 0 0 0 0 0 0 6.9749 -0.7700 -0.3189 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8359 0.4719 -0.8936 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2947 -2.2245 0.4494 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9501 -1.3428 -0.2384 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0025 -0.5243 1.9904 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1972 0.8297 2.9324 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6792 -0.0774 0.3023 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9564 -0.0417 1.9069 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2626 2.3886 0.3901 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4297 3.5779 1.2721 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5432 0.9356 2.6740 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4643 2.5830 3.3278 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8036 1.6076 0.6796 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9454 3.2511 1.3738 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9506 2.0540 2.1710 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7851 2.1929 3.5153 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9778 0.0996 3.5131 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7248 -0.0204 3.4979 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8366 -0.4714 1.0791 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4060 -1.7766 2.1470 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8046 -1.3057 1.3200 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6043 -1.8425 0.0838 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5271 1.0769 0.3572 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2677 0.3936 -0.7424 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8080 0.3890 0.3768 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.1282 0.4687 -0.3674 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.1231 -1.4422 -3.2266 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9100 -1.0317 -2.4912 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1314 -1.5331 -5.0423 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 1 0 9 10 2 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 8 38 1 0 9 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	MFQASGNLRRKBQG-HZJYTTRNSA-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/h2,6-7,9-10,18-20,24-25H,1,3-5,8,11-17H2/b7-6-,10-9-
SMILES	C=CCCC/C=CC/C=CCCCCCCCc1cc(O)cc(c1)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	342.26	Volume:	399.569 ? Van der Waals volume.
Dense:	0.857	LogP:	8.169 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	4.808 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-6.139 ? 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:	0.287	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	2.713	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:	0.688	Fluc inhibitor:	0.315 ? 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:	0.114 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.878	Promiscuous compounds:	0.084

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.282	MDCK Permeability:	-4.83
Pgp-inhibitor:	0.867	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%):	0.902	30% Bioavailability (F30%):	0.951
50% Bioavailability (F50%):	0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.026	MRP1:	0.994
Plasma Protein Binding (PPB):	98.405%	Volume Distribution (VD):	0.245
Fu:	0.907% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.272
OATP1B3 inhibitor:	0.73	BCRP inhibitor:	0.963
BSEP inhibitor:	0.997

ADMET: Metabolism

CYP1A2-inhibitor:	0.134	CYP1A2-substrate:	1.0
CYP2C19-inhibitor:	0.886	CYP2C19-substrate:	0.989
CYP2C9-inhibitor:	1.0	CYP2C9-substrate:	0.643
CYP2D6-inhibitor:	0.988	CYP2D6-substrate:	1.0
CYP3A4-inhibitor:	0.0	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.681	CYP2C8-inhibitor:	1.0
HLM stability:	0.952 ? 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):

5.135

Half-life (T1/2):

0.702

ADMET: Toxicity

hERG Blockers:	0.458	hERG Blockers (10um):	0.825
Human Hepatotoxicity (H-HT):	0.148	Drug-induced Liver Injury (DILI):	0.0
AMES Toxicity:	0.378	Rat Oral Acute Toxicity:	0.09
Maximum Recommended Daily Dose:	0.265	Skin Sensitization:	1.0
Carcinogencity:	0.041	Eye Corrosion:	0.997
Eye Irritation:	0.999	Respiratory Toxicity:	0.711
Drug-induced Neurotoxicity:	0.031	Ototoxicity:	0.091
Hematotoxicity:	0.002	Drug-induced Nephrotoxicity:	0.069
Genotoxicity:	0.0	RPMI-8226 Immunitoxicity:	0.044
A549 Cytotoxicity:	0.849	Hek293 Cytotoxicity:	0.71
BCF:	1.997 ? 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:	5.067 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.099 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	5.94 ? 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	2
IC90	1

Activity Type	# Activity
Organism	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
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	IC50	=	2.5	ug.mL-1	PMID[26890115]
NPT841	Organism	Leishmania major	Leishmania major	IC50	=	3.6	ug.mL-1	PMID[18519723]
NPT841	Organism	Leishmania major	Leishmania major	IC90	=	7.0	ug.mL-1	PMID[18519723]

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 NPC72947 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	31450
0.1-0.2	17255
0.2-0.3	965
0.3-0.4	94
0.4-0.5	38
0.5-0.6	17
0.6-0.7	16
0.7-0.8	0
0.8-0.85	12
0.85-0.9	0
0.9-0.95	1
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.9211	High Similarity	NPC10588
0.825	Intermediate Similarity	NPC71002
0.825	Intermediate Similarity	NPC302219
0.825	Intermediate Similarity	NPC242342
0.825	Intermediate Similarity	NPC249828
0.825	Intermediate Similarity	NPC85479
0.825	Intermediate Similarity	NPC284011
0.8108	Intermediate Similarity	NPC470700
0.8108	Intermediate Similarity	NPC54844
0.8108	Intermediate Similarity	NPC39097
0.8108	Intermediate Similarity	NPC302681
0.8108	Intermediate Similarity	NPC118286
0.8108	Intermediate Similarity	NPC109691
0.7692	Intermediate Similarity	NPC53051
0.7692	Intermediate Similarity	NPC24404
0.7692	Intermediate Similarity	NPC313030
0.7692	Intermediate Similarity	NPC39664
0.75	Intermediate Similarity	NPC146798
0.75	Intermediate Similarity	NPC222522
0.75	Intermediate Similarity	NPC106396
0.75	Intermediate Similarity	NPC94351
0.75	Intermediate Similarity	NPC168303
0.7143	Intermediate Similarity	NPC166761
0.6889	Remote Similarity	NPC192
0.6818	Remote Similarity	NPC204901
0.6486	Remote Similarity	NPC246056
0.617	Remote Similarity	NPC210497
0.6087	Remote Similarity	NPC158253
0.6	Remote Similarity	NPC305603
0.6	Remote Similarity	NPC61033
0.6	Remote Similarity	NPC294186
0.6	Remote Similarity	NPC147310
0.6	Remote Similarity	NPC127894
0.6	Remote Similarity	NPC137415
0.6	Remote Similarity	NPC166313
0.6	Remote Similarity	NPC192032
0.6	Remote Similarity	NPC24407
0.6	Remote Similarity	NPC470759
0.6	Remote Similarity	NPC11280
0.5849	Remote Similarity	NPC140521
0.5652	Remote Similarity	NPC483454
0.5652	Remote Similarity	NPC162314
0.56	Remote Similarity	NPC470760
0.5581	Remote Similarity	NPC241891
0.5581	Remote Similarity	NPC134829
0.5532	Remote Similarity	NPC94139
0.5532	Remote Similarity	NPC147284
0.5435	Remote Similarity	NPC232523
0.5319	Remote Similarity	NPC488413
0.5319	Remote Similarity	NPC488412
0.5294	Remote Similarity	NPC112596
0.5273	Remote Similarity	NPC123559
0.52	Remote Similarity	NPC48730
0.52	Remote Similarity	NPC219070
0.5106	Remote Similarity	NPC486908
0.5094	Remote Similarity	NPC249836

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC72947 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7139
0.1-0.2	1951
0.2-0.3	57
0.3-0.4	3
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