NPASS Compound

Natural Product: NPC493589

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 6.0265 0.5983 0.1352 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1521 -0.1802 -0.6580 O 0 0 0 0 0 0 0 0 0 0 0 0 3.7889 -0.2778 -0.4119 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2499 -1.2459 0.4091 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0954 -2.1646 1.0188 O 0 0 0 0 0 0 0 0 0 0 0 0 1.8758 -1.2868 0.6124 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0042 -0.4051 0.0348 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4378 -0.4029 0.2131 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0396 -1.3417 1.0191 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4134 -1.3499 1.1970 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9545 -2.1991 1.9258 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.1480 -0.3791 0.5328 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5225 -0.3294 0.6657 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1704 -1.2739 1.4820 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.2488 0.6318 0.0078 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5992 1.5595 -0.7957 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3928 2.5032 -1.4314 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2394 1.5157 -0.9312 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5089 0.5405 -0.2630 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2036 0.4772 -0.3767 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5568 0.5745 -0.7968 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9195 0.6166 -0.9997 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4614 1.5910 -1.8259 O 0 0 0 0 0 0 0 0 0 0 0 0 6.2853 1.5639 -0.3210 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4542 0.8279 1.0786 H 0 0 0 0 0 0 0 0 0 0 0 0 6.9118 0.0139 0.4626 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3662 -3.0402 0.5887 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4920 -2.0539 1.2575 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4865 -2.1051 1.5446 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2357 -2.2546 1.1992 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3222 0.6275 0.1451 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5015 2.6003 -2.4132 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7224 2.2368 -1.5573 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9255 1.2960 -1.2798 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5815 2.5157 -1.4682 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 4 6 1 0 6 7 2 0 7 8 1 0 8 9 2 0 9 10 1 0 10 11 2 0 10 12 1 0 12 13 2 0 13 14 1 0 13 15 1 0 15 16 2 0 16 17 1 0 16 18 1 0 18 19 2 0 19 20 1 0 7 21 1 0 21 22 2 0 22 23 1 0 22 3 1 0 20 8 1 0 19 12 1 0 1 24 1 0 1 25 1 0 1 26 1 0 5 27 1 0 6 28 1 0 9 29 1 0 14 30 1 0 15 31 1 0 17 32 1 0 18 33 1 0 21 34 1 0 23 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 NPC493589 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	29704
0.1-0.2	16865
0.2-0.3	2104
0.3-0.4	843
0.4-0.5	237
0.5-0.6	78
0.6-0.7	10
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	NPC601901
0.7925	Intermediate Similarity	NPC52005
0.7925	Intermediate Similarity	NPC606638
0.7358	Intermediate Similarity	NPC231772
0.7358	Intermediate Similarity	NPC62536
0.7358	Intermediate Similarity	NPC120464
0.7358	Intermediate Similarity	NPC483773
0.717	Intermediate Similarity	NPC123886
0.7143	Intermediate Similarity	NPC183950
0.7059	Intermediate Similarity	NPC175013
0.7037	Intermediate Similarity	NPC50403
0.6964	Remote Similarity	NPC12200
0.6607	Remote Similarity	NPC600900
0.6604	Remote Similarity	NPC279121
0.6538	Remote Similarity	NPC50898
0.6538	Remote Similarity	NPC78540
0.6102	Remote Similarity	NPC162351
0.6102	Remote Similarity	NPC609179
0.6094	Remote Similarity	NPC183
0.6066	Remote Similarity	NPC605634
0.6034	Remote Similarity	NPC256283
0.5965	Remote Similarity	NPC241498
0.5932	Remote Similarity	NPC82325
0.5932	Remote Similarity	NPC54394
0.5862	Remote Similarity	NPC100887
0.5789	Remote Similarity	NPC293183
0.5735	Remote Similarity	NPC150908
0.5735	Remote Similarity	NPC600972
0.5714	Remote Similarity	NPC274121
0.569	Remote Similarity	NPC284552
0.569	Remote Similarity	NPC184536
0.569	Remote Similarity	NPC156222
0.569	Remote Similarity	NPC103342
0.569	Remote Similarity	NPC605617
0.5652	Remote Similarity	NPC290830
0.5652	Remote Similarity	NPC71061
0.5652	Remote Similarity	NPC72425
0.5652	Remote Similarity	NPC303485
0.5614	Remote Similarity	NPC213216
0.5593	Remote Similarity	NPC286342
0.5593	Remote Similarity	NPC59951
0.5593	Remote Similarity	NPC610359
0.5574	Remote Similarity	NPC177298
0.5574	Remote Similarity	NPC223579
0.5571	Remote Similarity	NPC63454
0.5571	Remote Similarity	NPC183851
0.5571	Remote Similarity	NPC272064
0.5571	Remote Similarity	NPC186227
0.5538	Remote Similarity	NPC112954
0.5517	Remote Similarity	NPC610974
0.5493	Remote Similarity	NPC215203
0.5484	Remote Similarity	NPC133953
0.5484	Remote Similarity	NPC279989
0.5424	Remote Similarity	NPC301323
0.5424	Remote Similarity	NPC219330
0.5417	Remote Similarity	NPC601565
0.541	Remote Similarity	NPC83508
0.541	Remote Similarity	NPC255350
0.5405	Remote Similarity	NPC191306
0.5373	Remote Similarity	NPC34089
0.5373	Remote Similarity	NPC196179
0.5362	Remote Similarity	NPC134796
0.5333	Remote Similarity	NPC241838
0.5333	Remote Similarity	NPC234133
0.5333	Remote Similarity	NPC28274
0.5333	Remote Similarity	NPC188203
0.5323	Remote Similarity	NPC287101
0.5323	Remote Similarity	NPC603596
0.5323	Remote Similarity	NPC607642
0.5303	Remote Similarity	NPC301217
0.5263	Remote Similarity	NPC88023
0.5263	Remote Similarity	NPC172202
0.5263	Remote Similarity	NPC284127
0.5263	Remote Similarity	NPC309025
0.5254	Remote Similarity	NPC131624
0.5246	Remote Similarity	NPC108406
0.5238	Remote Similarity	NPC125062
0.5205	Remote Similarity	NPC265530
0.5167	Remote Similarity	NPC127447
0.5167	Remote Similarity	NPC29353
0.5167	Remote Similarity	NPC600177
0.5161	Remote Similarity	NPC212678
0.5161	Remote Similarity	NPC159103
0.5152	Remote Similarity	NPC138299
0.5152	Remote Similarity	NPC111112
0.5147	Remote Similarity	NPC254351
0.5132	Remote Similarity	NPC101731
0.5128	Remote Similarity	NPC600989
0.5082	Remote Similarity	NPC33265
0.5082	Remote Similarity	NPC184136
0.5082	Remote Similarity	NPC48479
0.5079	Remote Similarity	NPC160951
0.5075	Remote Similarity	NPC291746
0.5072	Remote Similarity	NPC224714
0.5072	Remote Similarity	NPC603692
0.5072	Remote Similarity	NPC610480
0.5068	Remote Similarity	NPC143851
0.5065	Remote Similarity	NPC165970
0.5063	Remote Similarity	NPC84324

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC493589 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5845
0.1-0.2	3242
0.2-0.3	53
0.3-0.4	7
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
0.6604	Remote Similarity	NPD1511	Phase 2
0.541	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