NPASS Compound

Natural Product: NPC542778

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 54 57 0 0 0 0 0 0 0 0999 V2000 -0.6110 0.2107 4.1627 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5980 0.1416 3.4218 O 0 0 0 0 0 0 0 0 0 0 0 0 0.6420 0.0892 2.0549 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5085 0.0998 1.2836 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5113 0.0488 -0.0892 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6260 0.0568 -0.8958 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9097 0.1177 -0.4444 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.7081 -0.9660 -0.8410 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.7316 -1.0833 0.0555 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.8275 -1.9209 -0.6024 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3001 -1.3398 -1.7523 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.2443 0.1706 0.6460 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.8769 0.2968 2.0063 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9185 1.4226 -0.0946 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.0101 1.8839 -0.8642 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.6868 1.3301 -0.9431 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.9251 2.4849 -0.9253 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7554 -0.0173 -0.6987 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9189 -0.0297 0.0354 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8528 0.0238 1.4108 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0535 0.0089 2.1136 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0352 0.0564 3.3704 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2300 -0.0582 1.3899 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2421 -0.1098 0.0177 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4905 -0.1820 -0.7770 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4030 -0.2316 -2.1702 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5458 -0.2984 -2.9221 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7883 -0.3179 -2.3277 C 0 0 0 0 0 0 0 0 0 0 0 0 8.9721 -0.3858 -3.0732 O 0 0 0 0 0 0 0 0 0 0 0 0 7.8997 -0.2697 -0.9495 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7348 -0.2029 -0.2182 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0899 -0.0934 -0.5992 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1560 -0.7376 4.0266 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4467 0.4235 5.2174 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2360 1.0114 3.7007 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4497 0.1517 1.8143 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9770 0.1632 0.6512 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3550 -1.7296 0.9027 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3887 -2.9225 -0.8489 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5946 -2.1099 0.1633 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6268 -2.0695 -2.3479 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3722 0.0975 0.6771 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9599 1.2615 2.2415 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7389 2.2324 0.6541 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7144 1.2162 -0.8261 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0106 1.0830 -1.9827 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1902 3.0119 -0.1326 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8158 -0.0597 -1.7827 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1645 -0.0700 1.9272 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4093 -0.2140 -2.5914 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4802 -0.3373 -4.0128 H 0 0 0 0 0 0 0 0 0 0 0 0 9.7697 -0.8871 -2.6908 H 0 0 0 0 0 0 0 0 0 0 0 0 8.8854 -0.2848 -0.4688 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8354 -0.1660 0.8498 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 1 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 9 12 1 0 12 13 1 0 12 14 1 0 14 15 1 0 14 16 1 0 16 17 1 0 5 18 2 0 18 19 1 0 19 20 2 0 20 21 1 0 21 22 2 0 21 23 1 0 23 24 2 0 24 25 1 0 25 26 2 0 26 27 1 0 27 28 2 0 28 29 1 0 28 30 1 0 30 31 2 0 24 32 1 0 20 3 1 0 31 25 1 0 16 7 1 0 32 19 1 0 1 33 1 0 1 34 1 0 1 35 1 0 4 36 1 0 7 37 1 1 9 38 1 1 10 39 1 0 10 40 1 0 11 41 1 0 12 42 1 1 13 43 1 0 14 44 1 1 15 45 1 0 16 46 1 6 17 47 1 0 18 48 1 0 23 49 1 0 26 50 1 0 27 51 1 0 29 52 1 0 30 53 1 0 31 54 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 NPC542778 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	23090
0.1-0.2	22495
0.2-0.3	2806
0.3-0.4	1001
0.4-0.5	327
0.5-0.6	94
0.6-0.7	27
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	NPC610763
0.7568	Intermediate Similarity	NPC83283
0.7333	Intermediate Similarity	NPC110349
0.7333	Intermediate Similarity	NPC39360
0.7333	Intermediate Similarity	NPC29763
0.7333	Intermediate Similarity	NPC210003
0.7317	Intermediate Similarity	NPC473512
0.7308	Intermediate Similarity	NPC284960
0.7273	Intermediate Similarity	NPC182045
0.7237	Intermediate Similarity	NPC93337
0.7143	Intermediate Similarity	NPC105025
0.6905	Remote Similarity	NPC129827
0.6795	Remote Similarity	NPC146792
0.6625	Remote Similarity	NPC100720
0.6582	Remote Similarity	NPC168822
0.6582	Remote Similarity	NPC95090
0.6582	Remote Similarity	NPC27408
0.6582	Remote Similarity	NPC189142
0.6582	Remote Similarity	NPC77660
0.65	Remote Similarity	NPC45638
0.6456	Remote Similarity	NPC58053
0.642	Remote Similarity	NPC222936
0.642	Remote Similarity	NPC201292
0.6386	Remote Similarity	NPC311830
0.6375	Remote Similarity	NPC259152
0.6296	Remote Similarity	NPC186807
0.6279	Remote Similarity	NPC473657
0.619	Remote Similarity	NPC479406
0.6125	Remote Similarity	NPC331652
0.6098	Remote Similarity	NPC58716
0.6071	Remote Similarity	NPC22832
0.6071	Remote Similarity	NPC243930
0.6071	Remote Similarity	NPC601144
0.6049	Remote Similarity	NPC261866
0.6049	Remote Similarity	NPC143851
0.6024	Remote Similarity	NPC27942
0.6	Remote Similarity	NPC602805
0.6	Remote Similarity	NPC607707
0.5976	Remote Similarity	NPC297987
0.5976	Remote Similarity	NPC323593
0.5976	Remote Similarity	NPC203500
0.5909	Remote Similarity	NPC295613
0.5904	Remote Similarity	NPC24043
0.5904	Remote Similarity	NPC84362
0.5854	Remote Similarity	NPC45618
0.5833	Remote Similarity	NPC599850
0.5824	Remote Similarity	NPC475497
0.5765	Remote Similarity	NPC479402
0.5765	Remote Similarity	NPC609451
0.5747	Remote Similarity	NPC479407
0.5714	Remote Similarity	NPC488080
0.5714	Remote Similarity	NPC169977
0.5698	Remote Similarity	NPC601710
0.5698	Remote Similarity	NPC605067
0.5652	Remote Similarity	NPC475366
0.5632	Remote Similarity	NPC88023
0.5632	Remote Similarity	NPC116458
0.5632	Remote Similarity	NPC246943
0.5632	Remote Similarity	NPC309025
0.5618	Remote Similarity	NPC472607
0.5595	Remote Similarity	NPC277205
0.5595	Remote Similarity	NPC37919
0.5595	Remote Similarity	NPC136042
0.5595	Remote Similarity	NPC609879
0.5542	Remote Similarity	NPC183357
0.5529	Remote Similarity	NPC84265
0.5506	Remote Similarity	NPC172807
0.5495	Remote Similarity	NPC15358
0.5484	Remote Similarity	NPC284277
0.5476	Remote Similarity	NPC77672
0.5476	Remote Similarity	NPC133671
0.5476	Remote Similarity	NPC19709
0.5476	Remote Similarity	NPC135391
0.5476	Remote Similarity	NPC78263
0.5476	Remote Similarity	NPC250069
0.5465	Remote Similarity	NPC117260
0.5435	Remote Similarity	NPC65003
0.5435	Remote Similarity	NPC607513
0.5412	Remote Similarity	NPC105511
0.5412	Remote Similarity	NPC161749
0.5402	Remote Similarity	NPC168584
0.5402	Remote Similarity	NPC191306
0.5402	Remote Similarity	NPC488071
0.5393	Remote Similarity	NPC601586
0.5349	Remote Similarity	NPC181712
0.5326	Remote Similarity	NPC44931
0.5287	Remote Similarity	NPC42773
0.5287	Remote Similarity	NPC45522
0.5281	Remote Similarity	NPC605784
0.5275	Remote Similarity	NPC8856
0.5233	Remote Similarity	NPC145038
0.5233	Remote Similarity	NPC8573
0.5233	Remote Similarity	NPC56077
0.5233	Remote Similarity	NPC197896
0.5233	Remote Similarity	NPC281131
0.5233	Remote Similarity	NPC313163
0.5233	Remote Similarity	NPC253662
0.5233	Remote Similarity	NPC179950
0.5233	Remote Similarity	NPC88789
0.5233	Remote Similarity	NPC491374
0.5227	Remote Similarity	NPC169404
0.5227	Remote Similarity	NPC307938
0.5227	Remote Similarity	NPC176186
0.5217	Remote Similarity	NPC603300
0.5211	Remote Similarity	NPC101294
0.5211	Remote Similarity	NPC278556
0.5208	Remote Similarity	NPC150767
0.5205	Remote Similarity	NPC47815
0.5172	Remote Similarity	NPC22195
0.5172	Remote Similarity	NPC245014
0.5172	Remote Similarity	NPC46420
0.5172	Remote Similarity	NPC10807
0.5172	Remote Similarity	NPC21190
0.5172	Remote Similarity	NPC161881
0.5169	Remote Similarity	NPC486578
0.5169	Remote Similarity	NPC606560
0.5158	Remote Similarity	NPC64425
0.5158	Remote Similarity	NPC64051
0.5116	Remote Similarity	NPC289667
0.5114	Remote Similarity	NPC198324
0.5114	Remote Similarity	NPC472459
0.5114	Remote Similarity	NPC205076
0.5111	Remote Similarity	NPC206123
0.5106	Remote Similarity	NPC3583
0.5102	Remote Similarity	NPC475382
0.51	Remote Similarity	NPC244875
0.5056	Remote Similarity	NPC282169
0.5055	Remote Similarity	NPC203050
0.5055	Remote Similarity	NPC469931
0.5055	Remote Similarity	NPC488072
0.5055	Remote Similarity	NPC225434
0.5055	Remote Similarity	NPC190003

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC542778 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5468
0.1-0.2	3574
0.2-0.3	90
0.3-0.4	11
0.4-0.5	5
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
0.551	Remote Similarity	NPD7472	Pre-clinical
0.5412	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