NPASS Compound

Natural Product: NPC545871

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 29 31 0 0 0 0 0 0 0 0999 V2000 0.1194 -1.6571 0.4315 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.2322 -0.4785 0.1451 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7114 0.4577 -0.2251 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0971 0.0785 -0.2815 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0324 0.9406 0.2751 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3570 0.5778 0.2210 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7784 -0.6046 -0.3637 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8102 -1.4159 -0.8967 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4603 -1.1082 -0.8746 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2707 1.7313 -0.5275 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0120 2.0585 -0.4687 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.9287 1.1879 -0.1198 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2318 1.5754 -0.0754 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1816 0.6310 0.2978 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5327 1.0010 0.3527 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.8366 -0.6540 0.6146 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5066 -1.0473 0.5686 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1415 -2.3475 0.8872 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5702 -0.1018 0.1966 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7646 1.8744 0.7437 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1219 1.2361 0.6513 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8339 -0.8400 -0.3782 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1383 -2.3439 -1.3558 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7653 -1.8058 -1.3184 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0060 2.4609 -0.8160 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5987 2.5567 -0.3052 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1473 0.4620 -0.2492 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5652 -1.4187 0.9120 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7817 -3.0066 0.2167 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 2 3 1 0 3 4 1 0 4 5 2 0 5 6 1 0 6 7 2 0 7 8 1 0 8 9 2 0 3 10 2 0 10 11 1 0 11 12 1 0 12 13 2 0 13 14 1 0 14 15 1 0 14 16 2 0 16 17 1 0 17 18 1 0 17 19 2 0 19 2 1 0 9 4 1 0 19 12 1 0 5 20 1 0 6 21 1 0 7 22 1 0 8 23 1 0 9 24 1 0 10 25 1 0 13 26 1 0 15 27 1 0 16 28 1 0 18 29 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 NPC545871 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	36817
0.1-0.2	11086
0.2-0.3	1462
0.3-0.4	329
0.4-0.5	105
0.5-0.6	35
0.6-0.7	12
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	NPC608554
0.8222	Intermediate Similarity	NPC39426
0.7609	Intermediate Similarity	NPC193792
0.75	Intermediate Similarity	NPC38065
0.7255	Intermediate Similarity	NPC294409
0.7255	Intermediate Similarity	NPC490701
0.68	Remote Similarity	NPC87545
0.6731	Remote Similarity	NPC78341
0.6667	Remote Similarity	NPC200316
0.6545	Remote Similarity	NPC194653
0.6429	Remote Similarity	NPC254702
0.6379	Remote Similarity	NPC608523
0.6316	Remote Similarity	NPC104728
0.625	Remote Similarity	NPC481044
0.6182	Remote Similarity	NPC239363
0.6071	Remote Similarity	NPC309154
0.6	Remote Similarity	NPC213659
0.6	Remote Similarity	NPC326109
0.5965	Remote Similarity	NPC279668
0.5965	Remote Similarity	NPC278323
0.5902	Remote Similarity	NPC606200
0.5893	Remote Similarity	NPC19980
0.5873	Remote Similarity	NPC474052
0.5862	Remote Similarity	NPC142876
0.5862	Remote Similarity	NPC483637
0.5862	Remote Similarity	NPC264550
0.5833	Remote Similarity	NPC238279
0.5806	Remote Similarity	NPC475705
0.5806	Remote Similarity	NPC233918
0.5781	Remote Similarity	NPC107838
0.5781	Remote Similarity	NPC600495
0.5714	Remote Similarity	NPC479305
0.5593	Remote Similarity	NPC476055
0.5593	Remote Similarity	NPC45291
0.5556	Remote Similarity	NPC268059
0.5538	Remote Similarity	NPC74178
0.5484	Remote Similarity	NPC85131
0.5484	Remote Similarity	NPC232947
0.5469	Remote Similarity	NPC128774
0.5417	Remote Similarity	NPC65060
0.541	Remote Similarity	NPC93552
0.541	Remote Similarity	NPC167595
0.5362	Remote Similarity	NPC156457
0.5303	Remote Similarity	NPC231763
0.5303	Remote Similarity	NPC482075
0.5303	Remote Similarity	NPC303197
0.5283	Remote Similarity	NPC234560
0.5263	Remote Similarity	NPC131266
0.5263	Remote Similarity	NPC269451
0.5224	Remote Similarity	NPC52889
0.5172	Remote Similarity	NPC303644
0.5102	Remote Similarity	NPC185497
0.5098	Remote Similarity	NPC201284

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC545871 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6644
0.1-0.2	2451
0.2-0.3	49
0.3-0.4	2
0.4-0.5	3
0.5-0.6	0
0.6-0.7	0
0.7-0.8	0
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8222	Intermediate Similarity	NPD1510	Phase 2

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