NPASS Compound

Natural Product: NPC522857

Natural Product ID	NPC522857
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Prosogerin A
IUPAC Name	2-(1,3-benzodioxol-5-yl)-7-hydroxy-6-methoxy-chromen-4-one
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 35 38 0 0 0 0 0 0 0 0999 V2000 6.1992 -0.4629 1.1923 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5582 -0.1625 -0.0043 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2124 -0.0825 -0.2075 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3311 -0.3082 0.8255 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9608 -0.2376 0.6639 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4247 0.0653 -0.5537 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2964 0.2978 -1.6143 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6668 0.2225 -1.4333 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5411 0.4533 -2.4871 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1314 0.1363 -0.7243 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7394 -0.0702 0.2274 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1900 0.0293 -0.0472 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5514 0.3455 -1.3379 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8806 0.4512 -1.6504 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8550 0.2524 -0.7208 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2478 0.3057 -0.8072 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.7751 0.2403 0.5053 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6725 -0.2080 1.2907 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4996 -0.0634 0.5687 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1488 -0.1768 0.9116 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2884 -0.3807 1.4853 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0873 -0.4638 1.6983 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5101 -0.7456 2.8387 O 0 0 0 0 0 0 0 0 0 0 0 0 7.1630 -0.9837 0.9338 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3845 0.4151 1.8454 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6228 -1.2055 1.7824 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6893 -0.5522 1.8135 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8695 0.5377 -2.5784 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7095 1.4258 -2.7340 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7668 0.5084 -2.0983 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1785 0.7010 -2.6691 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.5958 -0.5128 0.5020 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.1538 1.2164 0.8619 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8726 -0.4210 1.9087 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9420 -0.5665 2.3285 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 0 8 9 1 0 6 10 1 0 10 11 1 0 11 12 1 0 12 13 2 0 13 14 1 0 14 15 2 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 2 0 11 21 2 0 21 22 1 0 22 23 2 0 8 3 1 0 20 12 1 0 22 5 1 0 19 15 1 0 1 24 1 0 1 25 1 0 1 26 1 0 4 27 1 0 7 28 1 0 9 29 1 0 13 30 1 0 14 31 1 0 17 32 1 0 17 33 1 0 20 34 1 0 21 35 1 0 M END

Standard InCHIKey	MAKXJHCYKKCQQY-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C17H12O6/c1-20-16-5-10-11(18)6-14(23-15(10)7-12(16)19)9-2-3-13-17(4-9)22-8-21-13/h2-7,19H,8H2,1H3
SMILES	COC1=CC2=C(C=C1O)OC(C1=CC=C3OCOC3=C1)=CC2=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
NPO27221	Prosopis spicigera	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO27221	Prosopis spicigera	Species	Fabaceae	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 NPC522857 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	29154
0.1-0.2	17297
0.2-0.3	2702
0.3-0.4	514
0.4-0.5	161
0.5-0.6	25
0.6-0.7	5
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
0.6949	Remote Similarity	NPC312924
0.6462	Remote Similarity	NPC260640
0.6406	Remote Similarity	NPC605634
0.619	Remote Similarity	NPC604422
0.6032	Remote Similarity	NPC255350
0.5938	Remote Similarity	NPC256612
0.5738	Remote Similarity	NPC333230
0.5735	Remote Similarity	NPC269906
0.5571	Remote Similarity	NPC41853
0.5556	Remote Similarity	NPC77955
0.5538	Remote Similarity	NPC20830
0.5455	Remote Similarity	NPC283600
0.5455	Remote Similarity	NPC12200
0.5455	Remote Similarity	NPC115323
0.5455	Remote Similarity	NPC607642
0.5429	Remote Similarity	NPC167479
0.5312	Remote Similarity	NPC113089
0.5303	Remote Similarity	NPC69394
0.5278	Remote Similarity	NPC213622
0.5231	Remote Similarity	NPC266597
0.5224	Remote Similarity	NPC195202
0.5224	Remote Similarity	NPC606133
0.5152	Remote Similarity	NPC5167
0.5152	Remote Similarity	NPC256283
0.5143	Remote Similarity	NPC76482
0.5077	Remote Similarity	NPC205522
0.5077	Remote Similarity	NPC156222
0.5077	Remote Similarity	NPC608537
0.5075	Remote Similarity	NPC83508
0.507	Remote Similarity	NPC99671

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC522857 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5458
0.1-0.2	3569
0.2-0.3	118
0.3-0.4	3
0.4-0.5	1
0.5-0.6	0
0.6-0.7	1
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
0.6032	Remote Similarity	NPD2801	Pre-clinical

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