NPASS Compound

Natural Product: NPC502394

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 35 37 0 0 0 0 0 0 0 0999 V2000 6.6352 -0.2456 -0.6887 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5028 0.1593 -1.4367 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2103 0.0056 -0.9476 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1625 0.4265 -1.7401 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8948 0.2826 -1.2752 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6333 -0.2775 -0.0232 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2428 -0.4043 0.4189 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0849 -0.9424 1.6310 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4321 -1.0369 1.9974 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7708 -1.5271 3.1064 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4091 -0.5888 1.1372 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7514 -0.6523 1.4357 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1575 -1.1949 2.6667 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.6618 -0.1862 0.5281 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2719 0.3459 -0.6784 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3410 0.8361 -1.6194 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9495 0.4126 -0.9812 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0066 -0.0610 -0.0613 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7289 0.0016 -0.3500 O 0 0 0 0 0 0 0 0 0 0 0 0 2.6873 -0.6882 0.7463 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9742 -0.5406 0.2711 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5311 0.1161 0.3615 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7313 -1.3512 -0.6307 H 0 0 0 0 0 0 0 0 0 0 0 0 7.5691 0.1523 -1.0822 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3164 0.8662 -2.7169 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0360 0.5927 -1.8488 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6395 -1.3019 2.3282 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4881 -0.5848 3.4145 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7147 -0.2399 0.7706 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8684 1.0976 -2.5716 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0471 -0.0142 -1.7284 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8147 1.7261 -1.1408 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6343 0.8277 -1.9238 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5390 -1.1375 1.7433 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8269 -0.8704 0.8881 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 2 0 15 16 1 0 15 17 1 0 17 18 2 0 18 19 1 0 6 20 1 0 20 21 2 0 21 3 1 0 19 7 1 0 18 11 1 0 1 22 1 0 1 23 1 0 1 24 1 0 4 25 1 0 5 26 1 0 8 27 1 0 13 28 1 0 14 29 1 0 16 30 1 0 16 31 1 0 16 32 1 0 17 33 1 0 20 34 1 0 21 35 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 NPC502394 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	26208
0.1-0.2	19123
0.2-0.3	3572
0.3-0.4	690
0.4-0.5	196
0.5-0.6	50
0.6-0.7	7
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	NPC603662
0.7037	Intermediate Similarity	NPC29353
0.6909	Remote Similarity	NPC231772
0.6429	Remote Similarity	NPC156222
0.6316	Remote Similarity	NPC184136
0.6316	Remote Similarity	NPC57030
0.6316	Remote Similarity	NPC145379
0.614	Remote Similarity	NPC52611
0.614	Remote Similarity	NPC600177
0.5862	Remote Similarity	NPC274327
0.5862	Remote Similarity	NPC125887
0.5862	Remote Similarity	NPC127447
0.5806	Remote Similarity	NPC295036
0.5763	Remote Similarity	NPC176775
0.5763	Remote Similarity	NPC22519
0.5763	Remote Similarity	NPC234133
0.5763	Remote Similarity	NPC266597
0.5763	Remote Similarity	NPC604085
0.5763	Remote Similarity	NPC604462
0.5738	Remote Similarity	NPC195202
0.5738	Remote Similarity	NPC223579
0.5645	Remote Similarity	NPC610914
0.5507	Remote Similarity	NPC248739
0.55	Remote Similarity	NPC18260
0.5484	Remote Similarity	NPC52005
0.5484	Remote Similarity	NPC12200
0.5439	Remote Similarity	NPC604293
0.5429	Remote Similarity	NPC150908
0.541	Remote Similarity	NPC108406
0.541	Remote Similarity	NPC78913
0.5352	Remote Similarity	NPC303485
0.5352	Remote Similarity	NPC158027
0.5345	Remote Similarity	NPC101294
0.5345	Remote Similarity	NPC2771
0.5278	Remote Similarity	NPC14606
0.5278	Remote Similarity	NPC186227
0.5254	Remote Similarity	NPC14958
0.5246	Remote Similarity	NPC33265
0.5246	Remote Similarity	NPC48479
0.5246	Remote Similarity	NPC483773
0.5211	Remote Similarity	NPC601984
0.5205	Remote Similarity	NPC121649
0.5167	Remote Similarity	NPC293183
0.5161	Remote Similarity	NPC256283
0.5156	Remote Similarity	NPC137062
0.5147	Remote Similarity	NPC470402
0.5135	Remote Similarity	NPC18699
0.5135	Remote Similarity	NPC95090
0.5135	Remote Similarity	NPC27408
0.5135	Remote Similarity	NPC601565
0.5082	Remote Similarity	NPC241498
0.5082	Remote Similarity	NPC275722
0.5082	Remote Similarity	NPC239128
0.5079	Remote Similarity	NPC69394
0.5079	Remote Similarity	NPC212678
0.5079	Remote Similarity	NPC255350
0.5075	Remote Similarity	NPC602829
0.5072	Remote Similarity	NPC183
0.5067	Remote Similarity	NPC181712

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC502394 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4074
0.1-0.2	4878
0.2-0.3	187
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
0.5079	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