NPASS Compound

Natural Product: NPC298722

Natural Product ID	NPC298722
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	AAFWHAONVYRTMW-SREVYHEPSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	6440454
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 54 54 0 0 0 0 0 0 0 0999 V2000 7.7425 -0.6603 1.1820 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5279 -1.5638 1.3153 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7863 -1.5404 -0.0108 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3866 -0.0883 -0.2569 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6562 0.0733 -1.5178 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4339 0.5341 -1.5529 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6574 0.9355 -0.3760 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4146 0.0589 -0.3526 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5164 0.3503 0.7968 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0016 1.7616 0.8303 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7961 2.1441 -0.3715 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0161 1.3132 -0.6074 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9844 1.3881 0.5516 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1684 0.5596 0.2822 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1608 -0.7629 0.6765 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2559 -1.5961 0.4471 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3744 -1.0984 -0.1861 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.5777 -1.9343 -0.4617 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3891 0.2131 -0.5802 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3028 1.0235 -0.3478 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.5023 0.7546 -1.2240 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.2760 -2.9231 0.8307 O 0 0 0 0 0 0 0 0 0 0 0 0 7.4897 0.3622 1.5337 H 0 0 0 0 0 0 0 0 0 0 0 0 8.0807 -0.5854 0.1184 H 0 0 0 0 0 0 0 0 0 0 0 0 8.6072 -1.0877 1.7511 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8212 -2.6017 1.5581 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8479 -1.1139 2.0736 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4432 -1.8843 -0.8182 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8694 -2.1275 0.0273 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3940 0.4242 -0.4368 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0023 0.3867 0.6290 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2021 -0.2174 -2.4302 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9493 0.6277 -2.5491 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3689 2.0203 -0.4003 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1372 0.8015 0.6025 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8309 0.1627 -1.2909 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7128 -1.0075 -0.2901 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0897 0.1744 1.7333 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2964 -0.4027 0.7942 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8238 2.4936 0.9406 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6478 1.8939 1.7228 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1257 3.1951 -0.2381 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1545 2.1168 -1.2572 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7806 0.2588 -0.8804 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5445 1.7378 -1.4872 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5356 1.1240 1.5142 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3226 2.4433 0.6219 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3062 -1.1985 1.1766 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.1609 -1.4757 -1.2962 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.1958 -2.1061 0.4279 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.1867 -2.8985 -0.8807 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3122 2.0466 -0.6544 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.5230 0.7675 -2.2387 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8941 -3.2722 1.5755 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 2 0 6 7 1 0 7 8 1 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 2 0 15 16 1 0 16 17 2 0 17 18 1 0 17 19 1 0 19 20 2 0 19 21 1 0 16 22 1 0 20 14 1 0 1 23 1 0 1 24 1 0 1 25 1 0 2 26 1 0 2 27 1 0 3 28 1 0 3 29 1 0 4 30 1 0 4 31 1 0 5 32 1 0 6 33 1 0 7 34 1 0 7 35 1 0 8 36 1 0 8 37 1 0 9 38 1 0 9 39 1 0 10 40 1 0 10 41 1 0 11 42 1 0 11 43 1 0 12 44 1 0 12 45 1 0 13 46 1 0 13 47 1 0 15 48 1 0 18 49 1 0 18 50 1 0 18 51 1 0 20 52 1 0 21 53 1 0 22 54 1 0 M END

Standard InCHIKey	AAFWHAONVYRTMW-SREVYHEPSA-N
Standard InCHI	InChI=1S/C20H32O2/c1-3-4-5-6-7-8-9-10-11-12-13-14-18-15-19(21)17(2)20(22)16-18/h6-7,15-16,21-22H,3-5,8-14H2,1-2H3/b7-6-
SMILES	CCCC/C=CCCCCCCCc1cc(c(C)c(c1)O)O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	304.24	Volume:	352.954 ? Van der Waals volume.
Dense:	0.862	LogP:	7.854 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	4.641 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-5.014 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	11.0	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:	0.387	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	2.389	Fsp³:	0.6
MCE-18:	7.0 ? 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:	0.819	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:	0.152 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.951	Promiscuous compounds:	0.026

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.006	MDCK Permeability:	-4.673
Pgp-inhibitor:	0.99	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):	0.002
20% Bioavailability (F20%):	0.707	30% Bioavailability (F30%):	0.805
50% Bioavailability (F50%):	0.975

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.356	MRP1:	0.879
Plasma Protein Binding (PPB):	98.578%	Volume Distribution (VD):	0.026
Fu:	0.756% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.315
OATP1B3 inhibitor:	0.87	BCRP inhibitor:	0.824
BSEP inhibitor:	1.0

ADMET: Metabolism

CYP1A2-inhibitor:	0.001	CYP1A2-substrate:	0.977
CYP2C19-inhibitor:	0.999	CYP2C19-substrate:	0.996
CYP2C9-inhibitor:	1.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.292	CYP2D6-substrate:	0.999
CYP3A4-inhibitor:	0.119	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.298 ? 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):

5.888

Half-life (T1/2):

0.495

ADMET: Toxicity

hERG Blockers:	0.354	hERG Blockers (10um):	0.835
Human Hepatotoxicity (H-HT):	0.248	Drug-induced Liver Injury (DILI):	0.001
AMES Toxicity:	0.19	Rat Oral Acute Toxicity:	0.191
Maximum Recommended Daily Dose:	0.196	Skin Sensitization:	1.0
Carcinogencity:	0.033	Eye Corrosion:	0.983
Eye Irritation:	0.998	Respiratory Toxicity:	0.978
Drug-induced Neurotoxicity:	0.008	Ototoxicity:	0.178
Hematotoxicity:	0.012	Drug-induced Nephrotoxicity:	0.182
Genotoxicity:	0.0	RPMI-8226 Immunitoxicity:	0.117
A549 Cytotoxicity:	0.957	Hek293 Cytotoxicity:	0.798
BCF:	1.664 ? 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:	4.942 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.037 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	5.621 ? 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
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	whole plants	Sendai, Miyagi Prefecture, Japan	2000-Sep	PMID[17243725]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[17243725]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[17397219]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22940450]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3803	Ardisia japonica	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO3803	Ardisia japonica	Species	Primulaceae	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 NPC298722 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	27651
0.1-0.2	20099
0.2-0.3	1846
0.3-0.4	146
0.4-0.5	54
0.5-0.6	28
0.6-0.7	24
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
0.9706	High Similarity	NPC232523
0.8919	High Similarity	NPC158253
0.7949	Intermediate Similarity	NPC204901
0.7105	Intermediate Similarity	NPC53051
0.7105	Intermediate Similarity	NPC24404
0.7105	Intermediate Similarity	NPC313030
0.6923	Remote Similarity	NPC146798
0.6923	Remote Similarity	NPC222522
0.6923	Remote Similarity	NPC106396
0.6923	Remote Similarity	NPC94351
0.6923	Remote Similarity	NPC168303
0.6585	Remote Similarity	NPC488413
0.6585	Remote Similarity	NPC488412
0.6579	Remote Similarity	NPC470700
0.6579	Remote Similarity	NPC54844
0.6579	Remote Similarity	NPC39097
0.6579	Remote Similarity	NPC302681
0.6579	Remote Similarity	NPC118286
0.6579	Remote Similarity	NPC109691
0.6429	Remote Similarity	NPC71002
0.6429	Remote Similarity	NPC302219
0.6429	Remote Similarity	NPC249828
0.625	Remote Similarity	NPC39664
0.619	Remote Similarity	NPC483454
0.619	Remote Similarity	NPC162314
0.6053	Remote Similarity	NPC59506
0.6047	Remote Similarity	NPC94139
0.6047	Remote Similarity	NPC242342
0.6047	Remote Similarity	NPC85479
0.6047	Remote Similarity	NPC147284
0.5682	Remote Similarity	NPC10588
0.5682	Remote Similarity	NPC129373
0.5682	Remote Similarity	NPC488416
0.5652	Remote Similarity	NPC210497
0.5641	Remote Similarity	NPC37802
0.5581	Remote Similarity	NPC196479
0.5556	Remote Similarity	NPC72947
0.551	Remote Similarity	NPC305603
0.5455	Remote Similarity	NPC166761
0.5385	Remote Similarity	NPC294186
0.5385	Remote Similarity	NPC147310
0.5385	Remote Similarity	NPC137415
0.5385	Remote Similarity	NPC166313
0.5385	Remote Similarity	NPC192032
0.5385	Remote Similarity	NPC24407
0.5385	Remote Similarity	NPC11280
0.5349	Remote Similarity	NPC55561
0.5333	Remote Similarity	NPC284011
0.5319	Remote Similarity	NPC48730
0.525	Remote Similarity	NPC244513
0.5227	Remote Similarity	NPC487734
0.5208	Remote Similarity	NPC483450
0.52	Remote Similarity	NPC61033
0.5122	Remote Similarity	NPC488411
0.5122	Remote Similarity	NPC488410
0.5122	Remote Similarity	NPC488409
0.5116	Remote Similarity	NPC177420
0.5102	Remote Similarity	NPC470760

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC298722 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6168
0.1-0.2	2866
0.2-0.3	107
0.3-0.4	7
0.4-0.5	2
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