NPASS Compound

Natural Product: NPC486096

Natural Product ID	NPC486096
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	PDONMPUBRSPUSC-UHFFFAOYSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	44257866
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001615] Flavones [CHEMONTID:0003503] 6-prenylated flavones

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 44 46 0 0 0 0 0 0 0 0999 V2000 6.0450 -0.7158 -0.3294 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5420 0.4910 -0.2806 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4098 1.6981 -0.4317 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0965 0.7080 -0.0726 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4034 -0.6140 0.0463 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9361 -0.4727 0.2606 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4494 -0.1256 1.5007 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0852 -0.0107 1.6262 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7856 -0.2330 0.5521 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2712 -0.5793 -0.6778 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1345 -0.7971 -1.7326 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6607 -1.1092 -2.8395 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4786 -0.6472 -1.4654 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9712 -0.3002 -0.2266 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4086 -0.1422 0.0519 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8037 0.2031 1.3310 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1338 0.3618 1.6372 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.0980 0.1792 0.6728 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7322 -0.1680 -0.6213 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3861 -0.3170 -0.8848 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.4415 0.3341 0.9607 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.0860 -0.1106 0.7231 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0918 -0.6932 -0.8000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5699 -1.0475 -2.0708 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3024 0.1041 2.6006 O 0 0 0 0 0 0 0 0 0 0 0 0 3.9248 1.4831 1.0770 O 0 0 0 0 0 0 0 0 0 0 0 0 5.4370 -1.5975 -0.2228 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1287 -0.8202 -0.4856 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1912 1.7478 0.3543 H 0 0 0 0 0 0 0 0 0 0 0 0 6.9436 1.5731 -1.4104 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8378 2.6229 -0.4810 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6606 1.2837 -0.9219 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8205 -1.1761 0.8999 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5800 -1.2026 -0.8710 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3436 0.2643 2.5985 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1753 -0.8139 -2.2813 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0467 0.3480 2.0959 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4444 0.6299 2.6299 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.4586 -0.3218 -1.4120 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1189 -0.5859 -1.8917 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.8786 1.2395 0.7852 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5547 -2.0371 -2.2743 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6437 -0.7568 3.0409 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2039 2.1234 0.9440 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 2 3 1 0 2 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 2 0 11 13 1 0 13 14 2 0 14 15 1 0 15 16 2 0 16 17 1 0 17 18 2 0 18 19 1 0 19 20 2 0 18 21 1 0 14 22 1 0 10 23 2 0 23 24 1 0 7 25 1 0 4 26 1 0 23 6 1 0 22 9 1 0 20 15 1 0 1 27 1 0 1 28 1 0 3 29 1 0 3 30 1 0 3 31 1 0 4 32 1 0 5 33 1 0 5 34 1 0 8 35 1 0 13 36 1 0 16 37 1 0 17 38 1 0 19 39 1 0 20 40 1 0 21 41 1 0 24 42 1 0 25 43 1 0 26 44 1 0 M END

Standard InCHIKey	PDONMPUBRSPUSC-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C20H18O6/c1-10(2)14(22)7-13-15(23)8-18-19(20(13)25)16(24)9-17(26-18)11-3-5-12(21)6-4-11/h3-6,8-9,14,21-23,25H,1,7H2,2H3
SMILES	C=C(C)C(Cc1c(cc2c(c(=O)cc(c3ccc(cc3)O)o2)c1O)O)O

Calculated Properties

Physi-Chem Properties

MedChem Properties

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

ADMET: Distribution

ADMET: Metabolism

ADMET: Excretion

ADMET: Toxicity

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO40372	Tephrosia linearis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32155073]
NPO40372	Tephrosia linearis	Species	Fabaceae	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

Activity Type	# Activity
Activity	5

Activity Type	# Activity
Cell line	5

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
NPT927	Cell line	PBMC	Homo sapiens	Activity	=	103.28	%	PMID[32155073]
NPT927	Cell line	PBMC	Homo sapiens	Activity	=	57.64	%	PMID[32155073]
NPT927	Cell line	PBMC	Homo sapiens	Activity	=	238.54	%	PMID[32155073]
NPT927	Cell line	PBMC	Homo sapiens	Activity	=	38.92	%	PMID[32155073]
NPT927	Cell line	PBMC	Homo sapiens	Activity	=	5.2	%	PMID[32155073]

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 NPC486096 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	19660
0.1-0.2	26777
0.2-0.3	2547
0.3-0.4	677
0.4-0.5	157
0.5-0.6	35
0.6-0.7	2
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	Natural Product ID
0.7627	Intermediate Similarity	NPC284220
0.7419	Intermediate Similarity	NPC189706
0.6406	Remote Similarity	NPC3825
0.6119	Remote Similarity	NPC59210
0.597	Remote Similarity	NPC55018
0.5857	Remote Similarity	NPC33637
0.5833	Remote Similarity	NPC611357
0.5789	Remote Similarity	NPC476295
0.5775	Remote Similarity	NPC602497
0.5769	Remote Similarity	NPC479643
0.5763	Remote Similarity	NPC50898
0.5758	Remote Similarity	NPC24821
0.5735	Remote Similarity	NPC603717
0.5676	Remote Similarity	NPC66809
0.5676	Remote Similarity	NPC46736
0.5652	Remote Similarity	NPC14871
0.5634	Remote Similarity	NPC224714
0.5541	Remote Similarity	NPC328740
0.5541	Remote Similarity	NPC289774
0.5522	Remote Similarity	NPC270883
0.5484	Remote Similarity	NPC201395
0.5467	Remote Similarity	NPC476280
0.5467	Remote Similarity	NPC197856
0.5441	Remote Similarity	NPC482709
0.541	Remote Similarity	NPC130230
0.5385	Remote Similarity	NPC78913
0.5373	Remote Similarity	NPC220062
0.5325	Remote Similarity	NPC478511
0.5312	Remote Similarity	NPC241498
0.5312	Remote Similarity	NPC482122
0.5211	Remote Similarity	NPC301217
0.5211	Remote Similarity	NPC306488
0.52	Remote Similarity	NPC476350
0.5161	Remote Similarity	NPC222713
0.5072	Remote Similarity	NPC157784
0.5072	Remote Similarity	NPC67322
0.507	Remote Similarity	NPC476185
0.5067	Remote Similarity	NPC212932
0.5056	Remote Similarity	NPC479644

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC486096 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4946
0.1-0.2	4126
0.2-0.3	68
0.3-0.4	8
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