NPASS Compound

Natural Product: NPC609129

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 32 34 0 0 0 0 0 0 0 0999 V2000 6.1912 -0.0468 -0.1011 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2069 0.0949 -1.1021 O 0 0 0 0 0 0 0 0 0 0 0 0 3.8796 0.0466 -0.7314 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5469 -0.1353 0.5824 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2054 -0.1863 0.9730 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1912 -0.0563 0.0564 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1613 -0.1034 0.4190 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4760 -0.2697 1.6195 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1172 0.0333 -0.5471 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5092 -0.0118 -0.1985 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3825 0.9347 -0.7399 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7190 0.9055 -0.4161 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1970 -0.0524 0.4384 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5443 -0.0839 0.7664 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3286 -0.9837 0.9691 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9865 -0.9786 0.6629 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7069 0.2119 -1.8383 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5859 0.2537 -2.1613 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5358 0.1272 -1.2690 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8613 0.1801 -1.6726 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1755 0.1825 -0.6022 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2058 -1.0822 0.3230 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0612 0.6699 0.7386 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3283 -0.2395 1.3178 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9543 -0.3319 2.0240 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9553 1.6730 -1.4118 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3571 1.6550 -0.8569 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.2389 0.4080 0.2313 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6779 -1.7606 1.6536 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3013 -1.7005 1.0716 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4356 0.3244 -2.6337 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1655 0.3222 -2.7000 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 7 9 1 0 9 10 1 0 10 11 2 0 11 12 1 0 12 13 2 0 13 14 1 0 13 15 1 0 15 16 2 0 9 17 2 0 17 18 1 0 18 19 1 0 19 20 2 0 20 3 1 0 19 6 1 0 16 10 1 0 1 21 1 0 1 22 1 0 1 23 1 0 4 24 1 0 5 25 1 0 11 26 1 0 12 27 1 0 14 28 1 0 15 29 1 0 16 30 1 0 17 31 1 0 20 32 1 0 M END

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

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 NPC609129 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	26772
0.1-0.2	18747
0.2-0.3	3546
0.3-0.4	549
0.4-0.5	153
0.5-0.6	64
0.6-0.7	19
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC181124
0.78	Intermediate Similarity	NPC182428
0.7358	Intermediate Similarity	NPC605229
0.7037	Intermediate Similarity	NPC185607
0.6786	Remote Similarity	NPC162680
0.6786	Remote Similarity	NPC136095
0.6786	Remote Similarity	NPC303644
0.6786	Remote Similarity	NPC100971
0.6786	Remote Similarity	NPC209560
0.6786	Remote Similarity	NPC490700
0.6567	Remote Similarity	NPC211014
0.6491	Remote Similarity	NPC216769
0.6471	Remote Similarity	NPC161749
0.6441	Remote Similarity	NPC602183
0.6415	Remote Similarity	NPC234560
0.6316	Remote Similarity	NPC479067
0.6316	Remote Similarity	NPC216314
0.6316	Remote Similarity	NPC603503
0.623	Remote Similarity	NPC254741
0.6102	Remote Similarity	NPC471590
0.6034	Remote Similarity	NPC7013
0.6034	Remote Similarity	NPC269451
0.6	Remote Similarity	NPC12377
0.5932	Remote Similarity	NPC121522
0.5932	Remote Similarity	NPC609386
0.5902	Remote Similarity	NPC80710
0.5902	Remote Similarity	NPC139364
0.5893	Remote Similarity	NPC120924
0.5763	Remote Similarity	NPC10467
0.5763	Remote Similarity	NPC116632
0.5763	Remote Similarity	NPC333691
0.5763	Remote Similarity	NPC250266
0.5714	Remote Similarity	NPC218490
0.5692	Remote Similarity	NPC185401
0.5667	Remote Similarity	NPC69430
0.5667	Remote Similarity	NPC203747
0.5667	Remote Similarity	NPC610981
0.5645	Remote Similarity	NPC12175
0.5645	Remote Similarity	NPC191741
0.5625	Remote Similarity	NPC62518
0.5593	Remote Similarity	NPC474264
0.5556	Remote Similarity	NPC285973
0.5556	Remote Similarity	NPC55162
0.5556	Remote Similarity	NPC153008
0.5538	Remote Similarity	NPC600644
0.55	Remote Similarity	NPC131266
0.5493	Remote Similarity	NPC45165
0.5469	Remote Similarity	NPC478213
0.5455	Remote Similarity	NPC97716
0.5439	Remote Similarity	NPC125449
0.5417	Remote Similarity	NPC259070
0.5417	Remote Similarity	NPC478528
0.541	Remote Similarity	NPC186507
0.541	Remote Similarity	NPC124714
0.541	Remote Similarity	NPC269652
0.541	Remote Similarity	NPC294409
0.541	Remote Similarity	NPC490701
0.5397	Remote Similarity	NPC195763
0.5373	Remote Similarity	NPC219917
0.5352	Remote Similarity	NPC487214
0.5345	Remote Similarity	NPC242893
0.5342	Remote Similarity	NPC105511
0.5323	Remote Similarity	NPC181209
0.5323	Remote Similarity	NPC483565
0.5312	Remote Similarity	NPC200060
0.5312	Remote Similarity	NPC114192
0.5294	Remote Similarity	NPC611071
0.5286	Remote Similarity	NPC25547
0.5263	Remote Similarity	NPC229729
0.5254	Remote Similarity	NPC223354
0.5254	Remote Similarity	NPC195919
0.5246	Remote Similarity	NPC35763
0.5246	Remote Similarity	NPC474340
0.5238	Remote Similarity	NPC262623
0.5231	Remote Similarity	NPC35544
0.5224	Remote Similarity	NPC488135
0.5224	Remote Similarity	NPC607759
0.5211	Remote Similarity	NPC104406
0.5172	Remote Similarity	NPC39426
0.5156	Remote Similarity	NPC40290
0.5156	Remote Similarity	NPC90665
0.5143	Remote Similarity	NPC149875
0.5085	Remote Similarity	NPC324929
0.5079	Remote Similarity	NPC487217
0.5077	Remote Similarity	NPC134726
0.5072	Remote Similarity	NPC168085
0.5065	Remote Similarity	NPC43761

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC609129 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4453
0.1-0.2	4525
0.2-0.3	165
0.3-0.4	2
0.4-0.5	2
0.5-0.6	1
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	Drug ID	Developmental Stage
0.6471	Remote Similarity	NPD4381	Clinical (unspecified phase)
0.6316	Remote Similarity	NPD2796	Phase 2
0.5172	Remote Similarity	NPD1510	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