NPASS Compound

Natural Product: NPC604354

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 55 0 0 0 0 0 0 0 0999 V2000 -0.3841 -2.1196 3.2254 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2385 -1.5600 2.0862 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5365 -1.2354 0.9849 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8900 -1.4479 0.9845 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7005 -1.1328 -0.1092 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1397 -1.4309 0.0241 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.5922 -1.1675 1.3296 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9516 -0.6486 -0.9484 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.3160 -1.0232 -0.8750 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.8235 0.8279 -0.6341 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5269 1.6189 -1.5308 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.1315 -0.5956 -1.2171 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7724 -0.3680 -1.2509 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2052 0.1764 -2.3762 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0230 0.4941 -3.4798 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0092 -0.6858 -0.1609 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3855 -0.4616 -0.1776 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9730 0.7815 0.2242 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5103 1.3558 -0.8838 O 0 0 0 0 0 0 0 0 0 0 0 0 3.8090 1.0802 -1.1808 C 0 0 2 0 0 0 0 0 0 0 0 0 3.8603 -0.2248 -1.9426 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1546 -0.5748 -2.2823 O 0 0 0 0 0 0 0 0 0 0 0 0 4.7362 0.9994 -0.0107 C 0 0 1 0 0 0 0 0 0 0 0 0 5.9047 1.7175 -0.1479 O 0 0 0 0 0 0 0 0 0 0 0 0 4.0281 1.4951 1.2504 C 0 0 2 0 0 0 0 0 0 0 0 0 4.8703 1.4834 2.3404 O 0 0 0 0 0 0 0 0 0 0 0 0 2.8470 0.5617 1.3996 C 0 0 1 0 0 0 0 0 0 0 0 0 2.1443 0.8051 2.5761 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3571 -2.3668 4.0042 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9458 -3.0415 2.9881 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1092 -1.3761 3.6196 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3244 -1.8811 1.8865 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2913 -2.5192 -0.1545 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2427 -1.8437 1.5914 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6309 -0.8565 -1.9762 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8385 -0.2430 -0.5228 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7717 1.0869 -0.5355 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2745 0.9946 0.3869 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9025 2.2438 -1.9641 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7510 -0.3479 -2.0913 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6401 -0.3693 -3.8063 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3944 0.7884 -4.3513 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7108 1.3229 -3.2030 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1124 1.4305 0.5446 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1940 1.8626 -1.8622 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3607 -1.0249 -1.3443 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2423 -0.0635 -2.8709 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5573 -1.1218 -1.5727 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0020 -0.0585 0.1867 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7419 2.6916 -0.2279 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6470 2.5120 1.0059 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6020 2.2607 2.9163 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2268 -0.4979 1.3577 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3068 1.6969 2.9510 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 6 8 1 0 8 9 1 0 8 10 1 0 10 11 1 0 5 12 2 0 12 13 1 0 13 14 1 0 14 15 1 0 13 16 2 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 1 0 20 21 1 0 21 22 1 0 20 23 1 0 23 24 1 0 23 25 1 0 25 26 1 0 25 27 1 0 27 28 1 0 16 3 1 0 27 18 1 0 1 29 1 0 1 30 1 0 1 31 1 0 4 32 1 0 6 33 1 6 7 34 1 0 8 35 1 6 9 36 1 0 10 37 1 0 10 38 1 0 11 39 1 0 12 40 1 0 15 41 1 0 15 42 1 0 15 43 1 0 18 44 1 1 20 45 1 6 21 46 1 0 21 47 1 0 22 48 1 0 23 49 1 1 24 50 1 0 25 51 1 6 26 52 1 0 27 53 1 1 28 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 NPC604354 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	23284
0.1-0.2	22619
0.2-0.3	2956
0.3-0.4	678
0.4-0.5	245
0.5-0.6	49
0.6-0.7	15
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	3

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC48863
1.0	High Similarity	NPC251981
1.0	High Similarity	NPC13745
0.7347	Intermediate Similarity	NPC299144
0.7059	Intermediate Similarity	NPC69513
0.6792	Remote Similarity	NPC215833
0.6735	Remote Similarity	NPC217854
0.6667	Remote Similarity	NPC49074
0.6545	Remote Similarity	NPC162093
0.6471	Remote Similarity	NPC152722
0.6429	Remote Similarity	NPC210478
0.6271	Remote Similarity	NPC470236
0.6207	Remote Similarity	NPC95392
0.6207	Remote Similarity	NPC84013
0.6207	Remote Similarity	NPC55715
0.6207	Remote Similarity	NPC35877
0.62	Remote Similarity	NPC276195
0.619	Remote Similarity	NPC479447
0.6102	Remote Similarity	NPC232673
0.6	Remote Similarity	NPC95292
0.5763	Remote Similarity	NPC479029
0.5714	Remote Similarity	NPC166040
0.5714	Remote Similarity	NPC228907
0.569	Remote Similarity	NPC472024
0.566	Remote Similarity	NPC153149
0.5636	Remote Similarity	NPC608788
0.5556	Remote Similarity	NPC479030
0.5556	Remote Similarity	NPC25817
0.5538	Remote Similarity	NPC216129
0.5538	Remote Similarity	NPC130449
0.5538	Remote Similarity	NPC248132
0.5517	Remote Similarity	NPC218685
0.5469	Remote Similarity	NPC164857
0.5455	Remote Similarity	NPC190730
0.5424	Remote Similarity	NPC270849
0.5385	Remote Similarity	NPC475096
0.537	Remote Similarity	NPC192810
0.537	Remote Similarity	NPC294470
0.5357	Remote Similarity	NPC226712
0.5333	Remote Similarity	NPC26653
0.5333	Remote Similarity	NPC80600
0.5312	Remote Similarity	NPC486107
0.5283	Remote Similarity	NPC212729
0.5283	Remote Similarity	NPC604498
0.5263	Remote Similarity	NPC145900
0.5246	Remote Similarity	NPC248355
0.5231	Remote Similarity	NPC146803
0.5217	Remote Similarity	NPC51328
0.5217	Remote Similarity	NPC55158
0.5185	Remote Similarity	NPC269242
0.5179	Remote Similarity	NPC609376
0.5167	Remote Similarity	NPC479028
0.5167	Remote Similarity	NPC23084
0.5167	Remote Similarity	NPC479031
0.5161	Remote Similarity	NPC55040
0.5161	Remote Similarity	NPC104167
0.5152	Remote Similarity	NPC475084
0.5132	Remote Similarity	NPC486547
0.5088	Remote Similarity	NPC12308
0.5085	Remote Similarity	NPC40377
0.5085	Remote Similarity	NPC310661
0.5085	Remote Similarity	NPC9912
0.5082	Remote Similarity	NPC164599
0.5082	Remote Similarity	NPC65942
0.5082	Remote Similarity	NPC248307
0.5079	Remote Similarity	NPC302378
0.5079	Remote Similarity	NPC34456
0.5075	Remote Similarity	NPC485147
0.507	Remote Similarity	NPC199539

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC604354 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5751
0.1-0.2	3278
0.2-0.3	98
0.3-0.4	22
0.4-0.5	0
0.5-0.6	1
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	NPD1091	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