NPASS Compound

Natural Product: NPC91350

Natural Product ID	NPC91350
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	PPZYUSOIUGJLFB-OWOJBTEDSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	11142093
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0002699] Benzodioxanes [CHEMONTID:0002704] Phenylbenzodioxanes [CHEMONTID:0002707] Phenylbenzo-1,4-dioxanes

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 42 44 0 0 0 0 0 0 0 0999 V2000 4.6756 1.3360 0.1624 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5346 0.0630 -0.0821 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2428 -0.5938 -0.2299 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1988 -1.9565 -0.4898 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0039 -2.6241 -0.6380 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7930 -1.9702 -0.5352 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8334 -0.6040 -0.2747 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0384 0.0536 -0.1282 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3905 0.0680 -0.1687 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5315 -0.6089 -0.6767 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7666 0.1649 -0.5286 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9507 -0.3750 -0.0709 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0567 0.4463 0.0301 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0021 1.7961 -0.3173 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8147 2.3369 -0.7761 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7365 1.5069 -0.8673 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7766 3.6836 -1.1182 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.1170 2.6053 -0.2109 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5742 -1.9992 -0.1640 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4787 -2.1154 1.3375 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4571 -3.4975 1.6245 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4132 -2.6506 -0.6861 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0368 1.9445 0.3023 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2283 2.9437 -0.6629 O 0 0 0 0 0 0 0 0 0 0 0 0 3.8402 1.9823 0.2705 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4414 -0.5172 -0.1763 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1554 -2.4956 -0.5753 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0386 -3.6872 -0.8396 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0251 1.1131 0.0730 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3441 -0.6935 -1.7904 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0073 -1.4200 0.2022 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9799 0.0361 0.3843 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8025 1.9586 -1.2347 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3427 4.3032 -0.4167 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3522 3.0299 0.6769 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4626 -2.5075 -0.5578 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4997 -1.7344 1.6987 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2536 -1.5808 1.8817 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3684 -3.8470 1.7901 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1861 2.3877 1.3028 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7962 1.1615 0.1313 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4105 2.5577 -1.5573 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 2 0 6 7 1 0 7 8 2 0 7 9 1 0 9 10 1 0 10 11 1 0 11 12 2 0 12 13 1 0 13 14 2 0 14 15 1 0 15 16 2 0 15 17 1 0 14 18 1 0 10 19 1 0 19 20 1 0 20 21 1 0 19 22 1 0 1 23 1 0 23 24 1 0 8 3 1 0 16 11 1 0 22 6 1 0 1 25 1 0 2 26 1 0 4 27 1 0 5 28 1 0 8 29 1 0 10 30 1 0 12 31 1 0 13 32 1 0 16 33 1 0 17 34 1 0 18 35 1 0 19 36 1 0 20 37 1 0 20 38 1 0 21 39 1 0 23 40 1 0 23 41 1 0 24 42 1 0 M END

Standard InCHIKey	PPZYUSOIUGJLFB-OWOJBTEDSA-N
Standard InCHI	InChI=1S/C18H18O6/c19-7-1-2-11-3-6-15-16(8-11)24-18(17(10-20)23-15)12-4-5-13(21)14(22)9-12/h1-6,8-9,17-22H,7,10H2/b2-1+
SMILES	C(=Cc1ccc2c(c1)OC(c1ccc(c(c1)O)O)C(CO)O2)/CO

Calculated Properties

Physi-Chem Properties

Molecular Weight:	330.11	Volume:	328.501 ? Van der Waals volume.
Dense:	1.005	LogP:	1.323 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	1.674 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-2.698 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	4.0	Rigid Bonds:	18.0
TPSA:	99.38 ? Topological Polar Surface Area.	H-Bond Acceptor:	6.0
H-Bond Donor:	4.0	Rings:	3.0
Heavy Atoms:	6.0

MedChem Properties

QED Drug-Likeness Score:	0.64	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.376	Fsp³:	0.222
MCE-18:	54.091 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Rejected	GSK Rule:	Rejected
Golden Triangle Rule:	Rejected	BMS Rule:	0
Chelating Alert:	1	PAINS Alert:	1
Colloidal aggregators:	0.464	Fluc inhibitor:	0.416 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.061 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.442 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.63	Promiscuous compounds:	0.425

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.409	MDCK Permeability:	-4.86
Pgp-inhibitor:	0.06	Pgp-substrate:	0.005
PAMPA:	0.466 ? 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):	0.071
20% Bioavailability (F20%):	0.984	30% Bioavailability (F30%):	0.997
50% Bioavailability (F50%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.024	MRP1:	0.054
Plasma Protein Binding (PPB):	76.561%	Volume Distribution (VD):	-0.157
Fu:	24.728% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.903
OATP1B3 inhibitor:	0.999	BCRP inhibitor:	0.619
BSEP inhibitor:	0.911

ADMET: Metabolism

CYP1A2-inhibitor:	0.003	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	0.002	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	0.015	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.716	CYP2D6-substrate:	0.656
CYP3A4-inhibitor:	0.007	CYP3A4-substrate:	0.113
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.884
HLM stability:	0.118 ? 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):

13.759

Half-life (T1/2):

1.568

ADMET: Toxicity

hERG Blockers:	0.107	hERG Blockers (10um):	0.404
Human Hepatotoxicity (H-HT):	0.767	Drug-induced Liver Injury (DILI):	0.354
AMES Toxicity:	0.639	Rat Oral Acute Toxicity:	0.05
Maximum Recommended Daily Dose:	0.24	Skin Sensitization:	0.991
Carcinogencity:	0.506	Eye Corrosion:	0.008
Eye Irritation:	0.972	Respiratory Toxicity:	0.223
Drug-induced Neurotoxicity:	0.093	Ototoxicity:	0.686
Hematotoxicity:	0.05	Drug-induced Nephrotoxicity:	0.084
Genotoxicity:	0.42	RPMI-8226 Immunitoxicity:	0.017
A549 Cytotoxicity:	0.384	Hek293 Cytotoxicity:	0.208
BCF:	0.638 ? 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:	3.21 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.119 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.131 ? 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
NPO17551	Phytolacca americana	Species	Phytolaccaceae	Eukaryota	roots	n.a.	n.a.	PMID[18177012]
NPO17551	Phytolacca americana	Species	Phytolaccaceae	Eukaryota	Seeds	n.a.	n.a.	PMID[26595875]
NPO17551	Phytolacca americana	Species	Phytolaccaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO17551	Phytolacca americana	Species	Phytolaccaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO17551	Phytolacca americana	Species	Phytolaccaceae	Eukaryota	Shoot	n.a.	n.a.	Database[FooDB]
NPO17551	Phytolacca americana	Species	Phytolaccaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO17551	Phytolacca americana	Species	Phytolaccaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17551	Phytolacca americana	Species	Phytolaccaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17551	Phytolacca americana	Species	Phytolaccaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO17551	Phytolacca americana	Species	Phytolaccaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO17551	Phytolacca americana	Species	Phytolaccaceae	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 NPC91350 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	22049
0.1-0.2	23532
0.2-0.3	3926
0.3-0.4	282
0.4-0.5	42
0.5-0.6	10
0.6-0.7	6
0.7-0.8	0
0.8-0.85	0
0.85-0.9	1
0.9-0.95	1
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC72529
0.9388	High Similarity	NPC30083
0.8824	High Similarity	NPC488544
0.7736	Intermediate Similarity	NPC214729
0.7321	Intermediate Similarity	NPC479108
0.7069	Intermediate Similarity	NPC479113
0.6897	Remote Similarity	NPC471664
0.6897	Remote Similarity	NPC471665
0.6552	Remote Similarity	NPC83375
0.6271	Remote Similarity	NPC488545
0.6167	Remote Similarity	NPC55793
0.6	Remote Similarity	NPC488546
0.5763	Remote Similarity	NPC170694
0.5667	Remote Similarity	NPC479110
0.541	Remote Similarity	NPC114901
0.541	Remote Similarity	NPC48990
0.5373	Remote Similarity	NPC126206
0.52	Remote Similarity	NPC227894
0.5156	Remote Similarity	NPC147821
0.5156	Remote Similarity	NPC319625
0.5156	Remote Similarity	NPC183181
0.5156	Remote Similarity	NPC41706

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC91350 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4531
0.1-0.2	4496
0.2-0.3	113
0.3-0.4	7
0.4-0.5	3
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