NPASS Compound

Natural Product: NPC540615

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 36 38 0 0 0 0 0 0 0 0999 V2000 -4.8743 -2.8567 -0.6131 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6342 -1.5207 -0.2725 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3611 -1.0264 -0.1277 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2716 -1.8722 -0.3238 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9890 -1.3855 -0.1809 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8436 -0.0604 0.1556 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9401 0.7881 0.3522 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2097 0.2943 0.2076 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2967 1.1244 0.3998 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2202 2.4733 0.7411 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4388 0.4643 0.3081 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6234 1.6609 0.6127 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5419 -0.3351 0.1240 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8841 0.2139 0.2835 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8783 -0.4435 0.9830 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1489 0.0670 1.1390 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4617 1.2749 0.5863 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7303 1.8184 0.7237 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5121 1.9530 -0.1091 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2267 1.4351 -0.2662 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2914 -1.6496 -0.2114 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0767 -2.1223 -0.3498 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.9598 -3.0928 -0.5480 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3616 -3.5315 0.0970 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4829 -3.0983 -1.6282 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3824 -2.9143 -0.5883 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7817 1.8196 0.6148 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9102 3.0382 -0.1811 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2718 2.8092 0.9756 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5965 2.7018 1.6096 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6701 -1.3998 1.4340 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9303 -0.4529 1.6905 H 0 0 0 0 0 0 0 0 0 0 0 0 7.5669 1.2456 0.7175 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7857 2.9176 -0.5424 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4876 1.9772 -0.8153 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1326 -2.3149 -0.3659 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 9 10 1 0 6 11 1 0 11 12 2 0 11 13 1 0 13 14 1 0 14 15 2 0 15 16 1 0 16 17 2 0 17 18 1 0 17 19 1 0 19 20 2 0 13 21 2 0 21 22 1 0 8 3 1 0 20 14 1 0 22 5 1 0 1 23 1 0 1 24 1 0 1 25 1 0 4 26 1 0 7 27 1 0 10 28 1 0 10 29 1 0 10 30 1 0 15 31 1 0 16 32 1 0 18 33 1 0 19 34 1 0 20 35 1 0 21 36 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 NPC540615 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	27539
0.1-0.2	18341
0.2-0.3	3269
0.3-0.4	481
0.4-0.5	164
0.5-0.6	40
0.6-0.7	14
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	NPC605229
0.74	Intermediate Similarity	NPC120924
0.7358	Intermediate Similarity	NPC181124
0.7358	Intermediate Similarity	NPC100971
0.7037	Intermediate Similarity	NPC216769
0.6923	Remote Similarity	NPC195919
0.6909	Remote Similarity	NPC487217
0.6769	Remote Similarity	NPC259070
0.6667	Remote Similarity	NPC105511
0.6429	Remote Similarity	NPC186507
0.6429	Remote Similarity	NPC162680
0.6429	Remote Similarity	NPC303644
0.6333	Remote Similarity	NPC62518
0.6316	Remote Similarity	NPC148497
0.6296	Remote Similarity	NPC182842
0.625	Remote Similarity	NPC7013
0.625	Remote Similarity	NPC269451
0.6038	Remote Similarity	NPC234560
0.6	Remote Similarity	NPC285973
0.5965	Remote Similarity	NPC603503
0.5926	Remote Similarity	NPC218490
0.5862	Remote Similarity	NPC121522
0.5862	Remote Similarity	NPC209560
0.5862	Remote Similarity	NPC490700
0.569	Remote Similarity	NPC131266
0.5667	Remote Similarity	NPC12377
0.5636	Remote Similarity	NPC125449
0.5574	Remote Similarity	NPC139364
0.5538	Remote Similarity	NPC219917
0.5536	Remote Similarity	NPC182428
0.55	Remote Similarity	NPC181209
0.55	Remote Similarity	NPC279061
0.55	Remote Similarity	NPC483565
0.5455	Remote Similarity	NPC168085
0.5424	Remote Similarity	NPC10467
0.541	Remote Similarity	NPC52623
0.5357	Remote Similarity	NPC39426
0.5352	Remote Similarity	NPC211014
0.5333	Remote Similarity	NPC203747
0.5333	Remote Similarity	NPC609386
0.5333	Remote Similarity	NPC610981
0.5323	Remote Similarity	NPC80710
0.5278	Remote Similarity	NPC161749
0.5254	Remote Similarity	NPC185607
0.5238	Remote Similarity	NPC134726
0.5231	Remote Similarity	NPC260640
0.5211	Remote Similarity	NPC135345
0.5167	Remote Similarity	NPC116632
0.5167	Remote Similarity	NPC474340
0.5161	Remote Similarity	NPC262623
0.5152	Remote Similarity	NPC97716
0.5135	Remote Similarity	NPC205076
0.5082	Remote Similarity	NPC245382
0.5082	Remote Similarity	NPC136095
0.5082	Remote Similarity	NPC69430
0.5082	Remote Similarity	NPC294409
0.5082	Remote Similarity	NPC490701
0.5079	Remote Similarity	NPC487216
0.5079	Remote Similarity	NPC191741

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC540615 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4906
0.1-0.2	4114
0.2-0.3	121
0.3-0.4	4
0.4-0.5	3
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
0.5357	Remote Similarity	NPD1510	Phase 2
0.5278	Remote Similarity	NPD4381	Clinical (unspecified phase)

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