NPASS Compound

Natural Product: NPC603562

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 40 42 0 0 0 0 0 0 0 0999 V2000 6.9203 1.5754 0.0627 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5416 0.2195 -0.0035 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1780 -0.1091 -0.0549 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2285 0.8694 -0.0411 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9075 0.5481 -0.0909 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4529 -0.7697 -0.1577 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0053 -1.0031 -0.2075 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4550 -2.2661 -0.2747 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9117 -2.4269 -0.3192 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4126 -3.5681 -0.3800 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7276 -1.3269 -0.2966 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1087 -1.4259 -0.3390 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6714 -2.6920 -0.4067 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.9294 -0.3278 -0.3167 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3123 -0.4155 -0.3586 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.1322 -0.5131 0.7754 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3416 0.9110 -0.2494 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1392 2.0243 -0.2258 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.6405 3.3479 -0.1575 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9700 1.0169 -0.2070 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1237 -0.0683 -0.2281 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1627 0.0078 -0.1893 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3965 -1.7453 -0.1716 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7561 -1.4193 -0.1204 C 0 0 0 0 0 0 0 0 0 0 0 0 8.0246 1.6014 -0.1042 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3910 2.2122 -0.6792 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7570 2.0296 1.0577 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4912 1.9346 0.0100 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1659 1.3327 -0.0793 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1191 -3.1345 -0.2919 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0112 -3.0062 -1.2882 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9204 -1.2792 0.6625 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5378 -0.7898 1.6712 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6595 0.4642 0.9172 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2056 3.5635 0.8386 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4423 4.0668 -0.4152 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8122 3.5151 -0.8964 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5448 2.0050 -0.1546 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0962 -2.7762 -0.2222 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5052 -2.1824 -0.1310 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 2 0 9 11 1 0 11 12 2 0 12 13 1 0 12 14 1 0 14 15 1 0 15 16 1 0 14 17 2 0 17 18 1 0 18 19 1 0 17 20 1 0 20 21 2 0 21 22 1 0 6 23 1 0 23 24 2 0 24 3 1 0 22 7 1 0 21 11 1 0 1 25 1 0 1 26 1 0 1 27 1 0 4 28 1 0 5 29 1 0 8 30 1 0 13 31 1 0 16 32 1 0 16 33 1 0 16 34 1 0 19 35 1 0 19 36 1 0 19 37 1 0 20 38 1 0 23 39 1 0 24 40 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 NPC603562 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	27524
0.1-0.2	18737
0.2-0.3	2611
0.3-0.4	648
0.4-0.5	215
0.5-0.6	91
0.6-0.7	14
0.7-0.8	0
0.8-0.85	3
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	NPC145379
0.82	Intermediate Similarity	NPC239128
0.8077	Intermediate Similarity	NPC69394
0.8039	Intermediate Similarity	NPC120163
0.7925	Intermediate Similarity	NPC160951
0.7647	Intermediate Similarity	NPC75279
0.7547	Intermediate Similarity	NPC25270
0.7358	Intermediate Similarity	NPC276409
0.717	Intermediate Similarity	NPC156222
0.717	Intermediate Similarity	NPC29353
0.7143	Intermediate Similarity	NPC47781
0.7037	Intermediate Similarity	NPC110070
0.7037	Intermediate Similarity	NPC57030
0.6923	Remote Similarity	NPC58053
0.6909	Remote Similarity	NPC49824
0.6727	Remote Similarity	NPC176775
0.6716	Remote Similarity	NPC186807
0.6429	Remote Similarity	NPC184136
0.6429	Remote Similarity	NPC231772
0.6379	Remote Similarity	NPC608539
0.6316	Remote Similarity	NPC603662
0.625	Remote Similarity	NPC274327
0.6182	Remote Similarity	NPC14958
0.6164	Remote Similarity	NPC211594
0.614	Remote Similarity	NPC22519
0.6111	Remote Similarity	NPC604293
0.6102	Remote Similarity	NPC195202
0.5965	Remote Similarity	NPC52611
0.5965	Remote Similarity	NPC127447
0.5965	Remote Similarity	NPC600177
0.5932	Remote Similarity	NPC176300
0.5932	Remote Similarity	NPC255350
0.5882	Remote Similarity	NPC600396
0.5862	Remote Similarity	NPC33265
0.5862	Remote Similarity	NPC234133
0.5862	Remote Similarity	NPC266597
0.5862	Remote Similarity	NPC604085
0.5862	Remote Similarity	NPC604462
0.5833	Remote Similarity	NPC25495
0.5833	Remote Similarity	NPC93376
0.5833	Remote Similarity	NPC283600
0.5833	Remote Similarity	NPC223579
0.5833	Remote Similarity	NPC609451
0.5789	Remote Similarity	NPC293183
0.5769	Remote Similarity	NPC204693
0.5763	Remote Similarity	NPC163780
0.5763	Remote Similarity	NPC256283
0.5753	Remote Similarity	NPC605067
0.5714	Remote Similarity	NPC101294
0.5692	Remote Similarity	NPC470402
0.569	Remote Similarity	NPC241498
0.569	Remote Similarity	NPC275722
0.5667	Remote Similarity	NPC212678
0.5634	Remote Similarity	NPC93337
0.5593	Remote Similarity	NPC18260
0.5593	Remote Similarity	NPC198826
0.5593	Remote Similarity	NPC250266
0.5593	Remote Similarity	NPC101830
0.5588	Remote Similarity	NPC248739
0.5574	Remote Similarity	NPC177298
0.5574	Remote Similarity	NPC2476
0.5571	Remote Similarity	NPC272064
0.5556	Remote Similarity	NPC485299
0.5556	Remote Similarity	NPC483707
0.5556	Remote Similarity	NPC105025
0.5517	Remote Similarity	NPC607196
0.5517	Remote Similarity	NPC607530
0.5507	Remote Similarity	NPC601984
0.55	Remote Similarity	NPC108406
0.55	Remote Similarity	NPC78913
0.55	Remote Similarity	NPC18772
0.5484	Remote Similarity	NPC610914
0.5469	Remote Similarity	NPC76482
0.5439	Remote Similarity	NPC2771
0.5429	Remote Similarity	NPC158027
0.5417	Remote Similarity	NPC95090
0.5417	Remote Similarity	NPC27408
0.5397	Remote Similarity	NPC295036
0.5352	Remote Similarity	NPC14606
0.5342	Remote Similarity	NPC181712
0.5342	Remote Similarity	NPC45638
0.5342	Remote Similarity	NPC602537
0.5333	Remote Similarity	NPC100887
0.5333	Remote Similarity	NPC48479
0.5333	Remote Similarity	NPC231018
0.5325	Remote Similarity	NPC172807
0.5323	Remote Similarity	NPC196439
0.5323	Remote Similarity	NPC12200
0.5323	Remote Similarity	NPC608258
0.5278	Remote Similarity	NPC121649
0.5273	Remote Similarity	NPC226987
0.527	Remote Similarity	NPC201292
0.5254	Remote Similarity	NPC250822
0.5246	Remote Similarity	NPC162313
0.5238	Remote Similarity	NPC261004
0.5238	Remote Similarity	NPC137062
0.5205	Remote Similarity	NPC18699
0.5179	Remote Similarity	NPC30647
0.5172	Remote Similarity	NPC284424
0.5167	Remote Similarity	NPC284552
0.5167	Remote Similarity	NPC113089
0.5167	Remote Similarity	NPC125887
0.5167	Remote Similarity	NPC262094
0.5167	Remote Similarity	NPC609958
0.5161	Remote Similarity	NPC183597
0.5161	Remote Similarity	NPC83508
0.5156	Remote Similarity	NPC227192
0.5147	Remote Similarity	NPC213622
0.5132	Remote Similarity	NPC80188
0.5085	Remote Similarity	NPC333230
0.5085	Remote Similarity	NPC129680
0.5082	Remote Similarity	NPC62536
0.5082	Remote Similarity	NPC143828
0.5079	Remote Similarity	NPC52005
0.507	Remote Similarity	NPC150908
0.5065	Remote Similarity	NPC220169
0.5065	Remote Similarity	NPC602805
0.5063	Remote Similarity	NPC254540

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC603562 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4864
0.1-0.2	4128
0.2-0.3	147
0.3-0.4	8
0.4-0.5	2
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
0.5932	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