NPASS Compound

Natural Product: NPC551135

Natural Product ID	NPC551135
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	NCIOpen2_008608
IUPAC Name	3-(3,4-dimethoxyphenyl)allyl 3-(3,4-dimethoxyphenyl)prop-2-enoate
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds]

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 52 53 0 0 0 0 0 0 0 0999 V2000 6.6515 1.1059 -3.3212 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5753 -0.2706 -3.0047 O 0 0 0 0 0 0 0 0 0 0 0 0 5.3213 -0.8229 -2.7557 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1869 -0.0585 -2.8147 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9217 -0.6023 -2.5670 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7378 -1.9205 -2.2546 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4668 -2.5851 -2.0433 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2552 -2.2887 -2.2142 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4225 -1.1149 -2.7196 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2766 -0.5964 -1.6988 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6807 -0.1967 -0.5057 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5505 -0.3007 -0.3462 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4772 0.3573 0.5943 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7733 0.4789 0.4273 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6146 1.0209 1.4774 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9846 1.1619 1.2178 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8541 1.6747 2.1630 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4147 2.0693 3.4024 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2669 2.5841 4.3581 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.6455 2.7603 4.1728 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0602 1.9328 3.6693 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6171 2.3244 4.9081 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2851 2.2593 5.3704 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1717 1.4129 2.7131 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9249 -2.6831 -2.2000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1703 -2.1579 -2.4410 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3165 -2.9267 -2.3827 O 0 0 0 0 0 0 0 0 0 0 0 0 6.4203 -4.2785 -2.0910 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6887 1.4245 -3.5241 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9647 1.2723 -4.1997 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1808 1.6740 -2.4716 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2839 1.0052 -3.0626 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0804 0.0623 -2.6012 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6042 -3.6495 -1.5973 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4898 -3.1047 -1.9113 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1503 -1.4432 -3.5754 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1441 -0.3204 -3.1668 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9774 0.6485 1.5070 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2087 0.1571 -0.5298 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3290 0.8512 0.2482 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9108 1.7774 1.9390 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.8895 3.1295 3.1404 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.9554 3.6155 4.8428 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.2527 1.9039 4.4693 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2412 2.2738 6.4847 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6988 3.1139 5.0076 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8440 1.3107 4.9724 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1163 1.3194 2.9591 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8182 -3.7382 -1.9509 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4781 -4.7899 -2.3629 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2000 -4.7919 -2.7242 H 0 0 0 0 0 0 0 0 0 0 0 0 6.6666 -4.4454 -1.0064 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 2 0 6 7 1 0 7 8 2 3 8 9 1 0 9 10 1 0 10 11 1 0 11 12 2 0 11 13 1 0 13 14 2 3 14 15 1 0 15 16 2 0 16 17 1 0 17 18 2 0 18 19 1 0 19 20 1 0 18 21 1 0 21 22 1 0 22 23 1 0 21 24 2 0 6 25 1 0 25 26 2 0 26 27 1 0 27 28 1 0 26 3 1 0 24 15 1 0 1 29 1 0 1 30 1 0 1 31 1 0 4 32 1 0 5 33 1 0 7 34 1 0 8 35 1 0 9 36 1 0 9 37 1 0 13 38 1 0 14 39 1 0 16 40 1 0 17 41 1 0 20 42 1 0 20 43 1 0 20 44 1 0 23 45 1 0 23 46 1 0 23 47 1 0 24 48 1 0 25 49 1 0 28 50 1 0 28 51 1 0 28 52 1 0 M END

Standard InCHIKey	GRRDUNKIGVALCZ-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C22H24O6/c1-24-18-10-7-16(14-20(18)26-3)6-5-13-28-22(23)12-9-17-8-11-19(25-2)21(15-17)27-4/h5-12,14-15H,13H2,1-4H3
SMILES	COC1=CC=C(C=CCOC(=O)C=CC2=CC=C(OC)C(OC)=C2)C=C1OC

Calculated Properties

Physi-Chem Properties

Molecular Weight:	384.16	Volume:	400.968 ? Van der Waals volume.
Dense:	0.958	LogP:	3.429 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.412 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.573 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	10.0	Rigid Bonds:	15.0
TPSA:	63.22 ? Topological Polar Surface Area.	H-Bond Acceptor:	6.0
H-Bond Donor:	0.0	Rings:	2.0
Heavy Atoms:	6.0

MedChem Properties

QED Drug-Likeness Score:	0.481	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	2.171	Fsp³:	0.227
MCE-18:	13.0 ? 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:	Rejected
Golden Triangle Rule:	Rejected	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.993	Fluc inhibitor:	1.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.325 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.847 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.644	Promiscuous compounds:	0.322

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.739	MDCK Permeability:	-4.664
Pgp-inhibitor:	0.989	Pgp-substrate:	0.024
PAMPA:	0.009 ? 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):	0.412
20% Bioavailability (F20%):	0.93	30% Bioavailability (F30%):	0.821
50% Bioavailability (F50%):	0.988

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.006	MRP1:	0.301
Plasma Protein Binding (PPB):	88.244%	Volume Distribution (VD):	-0.084
Fu:	9.896% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.996
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.991
BSEP inhibitor:	1.0

ADMET: Metabolism

CYP1A2-inhibitor:	0.014	CYP1A2-substrate:	0.982
CYP2C19-inhibitor:	0.135	CYP2C19-substrate:	0.856
CYP2C9-inhibitor:	0.591	CYP2C9-substrate:	0.168
CYP2D6-inhibitor:	0.999	CYP2D6-substrate:	0.996
CYP3A4-inhibitor:	0.32	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	0.915 ? 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):

8.647

Half-life (T1/2):

1.001

ADMET: Toxicity

hERG Blockers:	0.337	hERG Blockers (10um):	0.728
Human Hepatotoxicity (H-HT):	0.195	Drug-induced Liver Injury (DILI):	0.225
AMES Toxicity:	0.646	Rat Oral Acute Toxicity:	0.16
Maximum Recommended Daily Dose:	0.379	Skin Sensitization:	0.985
Carcinogencity:	0.651	Eye Corrosion:	0.021
Eye Irritation:	0.654	Respiratory Toxicity:	0.234
Drug-induced Neurotoxicity:	0.541	Ototoxicity:	0.249
Hematotoxicity:	0.061	Drug-induced Nephrotoxicity:	0.518
Genotoxicity:	0.009	RPMI-8226 Immunitoxicity:	0.136
A549 Cytotoxicity:	0.118	Hek293 Cytotoxicity:	0.489
BCF:	1.089 ? 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:	3.895 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.241 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.724 ? 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
NPO51476	Baccharis viminea	Genus	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]

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 NPC551135 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	23119
0.1-0.2	23229
0.2-0.3	2995
0.3-0.4	408
0.4-0.5	82
0.5-0.6	15
0.6-0.7	6
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
0.878	High Similarity	NPC277460
0.7045	Intermediate Similarity	NPC38403
0.6739	Remote Similarity	NPC246704
0.62	Remote Similarity	NPC237131
0.619	Remote Similarity	NPC179686
0.6122	Remote Similarity	NPC159916
0.6098	Remote Similarity	NPC208183
0.6098	Remote Similarity	NPC243289
0.5897	Remote Similarity	NPC310905
0.5778	Remote Similarity	NPC212643
0.5652	Remote Similarity	NPC288238
0.561	Remote Similarity	NPC179309
0.5532	Remote Similarity	NPC27352
0.5476	Remote Similarity	NPC222175
0.5455	Remote Similarity	NPC473909
0.5435	Remote Similarity	NPC94347
0.5385	Remote Similarity	NPC204466
0.5349	Remote Similarity	NPC245552
0.5349	Remote Similarity	NPC227894
0.5349	Remote Similarity	NPC185738
0.5306	Remote Similarity	NPC202474
0.5156	Remote Similarity	NPC482417
0.5102	Remote Similarity	NPC260952

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC551135 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4211
0.1-0.2	4717
0.2-0.3	207
0.3-0.4	12
0.4-0.5	1
0.5-0.6	2
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
0.5532	Remote Similarity	NPD1358	Phase 4
0.5349	Remote Similarity	NPD5536	Phase 2

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