NPASS Compound

Natural Product: NPC602306

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 38 40 0 0 0 0 0 0 0 0999 V2000 -5.8631 1.3239 -1.0396 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1176 0.5941 -0.1169 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.7256 0.5359 -0.2175 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1188 1.2100 -1.2392 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7166 1.1443 -1.3305 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9309 0.4503 -0.4632 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5215 0.3326 -0.4884 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1113 -0.4082 0.4699 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3949 -0.5836 0.5474 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9735 -1.3551 1.5500 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3341 -1.5442 1.6366 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8607 -2.3260 2.6605 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1536 -0.9509 0.7004 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5804 -0.1729 -0.3121 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3618 0.4404 -1.2714 O 0 0 0 0 0 0 0 0 0 0 0 0 3.2111 0.0095 -0.3881 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6986 0.7817 -1.4005 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3906 1.3410 -2.2725 O 0 0 0 0 0 0 0 0 0 0 0 0 1.2962 0.9284 -1.4223 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7919 1.6955 -2.4285 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6336 -0.2196 0.5652 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9834 -0.1939 0.7056 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6685 -0.8536 1.7174 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8905 -1.5894 2.6443 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8882 1.4898 -0.6021 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0336 0.7843 -1.9926 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4551 2.3401 -1.2457 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6334 1.7942 -1.9886 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2352 1.6762 -2.1370 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3324 -1.8185 2.2815 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5229 -1.8960 3.3089 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2300 -1.0705 0.7268 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8727 -0.0494 -1.9949 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2838 2.3203 -3.0199 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0704 -0.7915 1.2911 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1928 -2.2867 2.1418 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5004 -2.1853 3.3389 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2644 -0.8971 3.2525 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 1 0 8 9 1 0 9 10 2 0 10 11 1 0 11 12 1 0 11 13 2 0 13 14 1 0 14 15 1 0 14 16 2 0 16 17 1 0 17 18 2 0 17 19 1 0 19 20 1 0 6 21 1 0 21 22 2 0 22 23 1 0 23 24 1 0 22 3 1 0 19 7 2 0 16 9 1 0 1 25 1 0 1 26 1 0 1 27 1 0 4 28 1 0 5 29 1 0 10 30 1 0 12 31 1 0 13 32 1 0 15 33 1 0 20 34 1 0 21 35 1 0 24 36 1 0 24 37 1 0 24 38 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 NPC602306 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	27613
0.1-0.2	18821
0.2-0.3	2329
0.3-0.4	818
0.4-0.5	187
0.5-0.6	65
0.6-0.7	10
0.7-0.8	0
0.8-0.85	1
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	NPC159103
0.8077	Intermediate Similarity	NPC241838
0.7885	Intermediate Similarity	NPC219330
0.7778	Intermediate Similarity	NPC54394
0.75	Intermediate Similarity	NPC125062
0.7455	Intermediate Similarity	NPC166753
0.7407	Intermediate Similarity	NPC28274
0.7321	Intermediate Similarity	NPC12200
0.7321	Intermediate Similarity	NPC603596
0.7321	Intermediate Similarity	NPC609179
0.7091	Intermediate Similarity	NPC50403
0.6897	Remote Similarity	NPC133953
0.6842	Remote Similarity	NPC50728
0.6667	Remote Similarity	NPC179271
0.6604	Remote Similarity	NPC116775
0.6604	Remote Similarity	NPC187432
0.6481	Remote Similarity	NPC20791
0.6441	Remote Similarity	NPC224137
0.6271	Remote Similarity	NPC602344
0.6182	Remote Similarity	NPC169749
0.6167	Remote Similarity	NPC261548
0.5932	Remote Similarity	NPC59951
0.5932	Remote Similarity	NPC231772
0.5932	Remote Similarity	NPC62536
0.5932	Remote Similarity	NPC610359
0.5902	Remote Similarity	NPC200316
0.5902	Remote Similarity	NPC606638
0.5873	Remote Similarity	NPC605634
0.5833	Remote Similarity	NPC134677
0.5797	Remote Similarity	NPC171821
0.5789	Remote Similarity	NPC216361
0.5763	Remote Similarity	NPC44079
0.5738	Remote Similarity	NPC200740
0.5738	Remote Similarity	NPC82325
0.569	Remote Similarity	NPC256042
0.5672	Remote Similarity	NPC183
0.5667	Remote Similarity	NPC201451
0.5667	Remote Similarity	NPC143799
0.5645	Remote Similarity	NPC52005
0.5645	Remote Similarity	NPC162351
0.5614	Remote Similarity	NPC601197
0.5574	Remote Similarity	NPC49824
0.5556	Remote Similarity	NPC254306
0.5556	Remote Similarity	NPC252933
0.55	Remote Similarity	NPC184536
0.55	Remote Similarity	NPC103342
0.55	Remote Similarity	NPC152042
0.5484	Remote Similarity	NPC115798
0.5484	Remote Similarity	NPC255350
0.541	Remote Similarity	NPC286342
0.541	Remote Similarity	NPC87125
0.541	Remote Similarity	NPC281207
0.541	Remote Similarity	NPC120464
0.541	Remote Similarity	NPC483773
0.5397	Remote Similarity	NPC93376
0.5397	Remote Similarity	NPC236769
0.5397	Remote Similarity	NPC195202
0.5397	Remote Similarity	NPC604422
0.5397	Remote Similarity	NPC610401
0.5373	Remote Similarity	NPC200694
0.5333	Remote Similarity	NPC21100
0.5333	Remote Similarity	NPC26227
0.5323	Remote Similarity	NPC86485
0.5323	Remote Similarity	NPC600900
0.5312	Remote Similarity	NPC183950
0.5312	Remote Similarity	NPC279989
0.5246	Remote Similarity	NPC123886
0.5246	Remote Similarity	NPC98661
0.5238	Remote Similarity	NPC55205
0.5231	Remote Similarity	NPC227192
0.5231	Remote Similarity	NPC483775
0.5224	Remote Similarity	NPC205046
0.5195	Remote Similarity	NPC197285
0.5161	Remote Similarity	NPC601901
0.5161	Remote Similarity	NPC605755
0.5156	Remote Similarity	NPC602125
0.5152	Remote Similarity	NPC607815
0.5147	Remote Similarity	NPC130955
0.5143	Remote Similarity	NPC479305
0.5128	Remote Similarity	NPC88023
0.5128	Remote Similarity	NPC165970
0.5128	Remote Similarity	NPC136761
0.5128	Remote Similarity	NPC309025
0.5128	Remote Similarity	NPC606270
0.5077	Remote Similarity	NPC604021
0.5063	Remote Similarity	NPC288131

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC602306 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5115
0.1-0.2	3952
0.2-0.3	74
0.3-0.4	5
0.4-0.5	1
0.5-0.6	1
0.6-0.7	1
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
0.6481	Remote Similarity	NPD1512	Phase 3
0.5484	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