NPASS Compound

Natural Product: NPC612000

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 36 0 0 0 0 0 0 0 0999 V2000 -2.5203 2.9169 1.8041 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0249 1.6242 1.5946 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3704 0.9771 0.3882 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.0494 0.9059 0.6070 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3209 -0.0459 -0.0508 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8896 -0.2085 0.6445 O 0 0 0 0 0 0 0 0 0 0 0 0 2.1611 -0.0557 0.1615 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2277 -0.2678 1.0316 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5415 -0.1382 0.6387 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8665 0.2128 -0.6537 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1906 0.3491 -1.0711 O 0 0 0 0 0 0 0 0 0 0 0 0 3.8200 0.4252 -1.5237 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4822 0.2946 -1.1287 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9826 -1.4085 -0.0749 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.1344 -2.2872 -0.7254 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2941 -1.2254 -0.8104 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.9953 -2.4142 -0.9440 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0981 -0.2843 0.0821 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.3402 -0.0293 -0.4778 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.6360 3.3999 0.9478 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8073 0.9610 2.4682 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1202 1.6297 1.4296 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5565 1.6844 -0.4727 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1661 0.2395 -1.1095 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9905 -0.5458 2.0568 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3746 -0.3068 1.3294 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8126 0.9663 -0.5454 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0514 0.7049 -2.5555 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6840 0.4689 -1.8383 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1961 -1.6899 0.9731 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0529 -3.0280 -0.1211 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1544 -0.6871 -1.7678 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7795 -2.9649 -0.1416 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2674 -0.8352 1.0321 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3310 0.6621 -1.1771 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 2 0 8 9 1 0 9 10 2 0 10 11 1 0 10 12 1 0 12 13 2 0 5 14 1 0 14 15 1 0 14 16 1 0 16 17 1 0 16 18 1 0 18 19 1 0 18 3 1 0 13 7 1 0 1 20 1 0 2 21 1 0 2 22 1 0 3 23 1 6 5 24 1 6 8 25 1 0 9 26 1 0 11 27 1 0 12 28 1 0 13 29 1 0 14 30 1 1 15 31 1 0 16 32 1 6 17 33 1 0 18 34 1 1 19 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 NPC612000 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	17296
0.1-0.2	27892
0.2-0.3	3313
0.3-0.4	759
0.4-0.5	438
0.5-0.6	106
0.6-0.7	31
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	NPC142319
0.72	Intermediate Similarity	NPC57751
0.7021	Intermediate Similarity	NPC221090
0.6818	Remote Similarity	NPC212729
0.6818	Remote Similarity	NPC604498
0.6739	Remote Similarity	NPC9248
0.6735	Remote Similarity	NPC40377
0.6667	Remote Similarity	NPC269242
0.6667	Remote Similarity	NPC484157
0.6667	Remote Similarity	NPC228907
0.6522	Remote Similarity	NPC153149
0.6522	Remote Similarity	NPC192810
0.6522	Remote Similarity	NPC294470
0.6471	Remote Similarity	NPC83975
0.6458	Remote Similarity	NPC12308
0.6444	Remote Similarity	NPC276195
0.6383	Remote Similarity	NPC25817
0.6383	Remote Similarity	NPC152722
0.6346	Remote Similarity	NPC214910
0.6346	Remote Similarity	NPC26080
0.6346	Remote Similarity	NPC165686
0.6327	Remote Similarity	NPC192229
0.6327	Remote Similarity	NPC145900
0.6304	Remote Similarity	NPC217854
0.625	Remote Similarity	NPC60589
0.625	Remote Similarity	NPC469708
0.625	Remote Similarity	NPC604439
0.625	Remote Similarity	NPC609376
0.62	Remote Similarity	NPC214454
0.6122	Remote Similarity	NPC200092
0.6	Remote Similarity	NPC85799
0.6	Remote Similarity	NPC303422
0.6	Remote Similarity	NPC97326
0.6	Remote Similarity	NPC80098
0.5882	Remote Similarity	NPC166168
0.5862	Remote Similarity	NPC121001
0.5849	Remote Similarity	NPC205054
0.5849	Remote Similarity	NPC23084
0.5818	Remote Similarity	NPC198487
0.5769	Remote Similarity	NPC310661
0.5667	Remote Similarity	NPC259767
0.5667	Remote Similarity	NPC99233
0.5667	Remote Similarity	NPC57587
0.5636	Remote Similarity	NPC473044
0.5614	Remote Similarity	NPC478871
0.5614	Remote Similarity	NPC478870
0.5614	Remote Similarity	NPC478872
0.5614	Remote Similarity	NPC233559
0.5614	Remote Similarity	NPC478873
0.5574	Remote Similarity	NPC92054
0.5574	Remote Similarity	NPC601828
0.5556	Remote Similarity	NPC251102
0.5556	Remote Similarity	NPC210298
0.5556	Remote Similarity	NPC19470
0.5556	Remote Similarity	NPC604356
0.5536	Remote Similarity	NPC222455
0.5536	Remote Similarity	NPC106025
0.5517	Remote Similarity	NPC242028
0.5517	Remote Similarity	NPC294166
0.5517	Remote Similarity	NPC203230
0.5517	Remote Similarity	NPC252169
0.5517	Remote Similarity	NPC115022
0.549	Remote Similarity	NPC226712
0.549	Remote Similarity	NPC608788
0.5484	Remote Similarity	NPC271479
0.5455	Remote Similarity	NPC210015
0.5455	Remote Similarity	NPC164599
0.5455	Remote Similarity	NPC481303
0.5439	Remote Similarity	NPC59324
0.5439	Remote Similarity	NPC473045
0.5439	Remote Similarity	NPC218003
0.5439	Remote Similarity	NPC65833
0.5424	Remote Similarity	NPC37074
0.5424	Remote Similarity	NPC8497
0.5424	Remote Similarity	NPC185778
0.541	Remote Similarity	NPC177742
0.5397	Remote Similarity	NPC308265
0.5397	Remote Similarity	NPC170475
0.5385	Remote Similarity	NPC97240
0.5385	Remote Similarity	NPC160882
0.537	Remote Similarity	NPC218685
0.5357	Remote Similarity	NPC105827
0.5345	Remote Similarity	NPC199335
0.5345	Remote Similarity	NPC475628
0.5345	Remote Similarity	NPC477240
0.5333	Remote Similarity	NPC260681
0.5333	Remote Similarity	NPC60756
0.5333	Remote Similarity	NPC287780
0.5333	Remote Similarity	NPC60982
0.5323	Remote Similarity	NPC165720
0.5323	Remote Similarity	NPC148273
0.5312	Remote Similarity	NPC39351
0.5294	Remote Similarity	NPC299144
0.5283	Remote Similarity	NPC166040
0.5283	Remote Similarity	NPC604209
0.5273	Remote Similarity	NPC479028
0.5273	Remote Similarity	NPC479031
0.5273	Remote Similarity	NPC606892
0.5263	Remote Similarity	NPC25292
0.5263	Remote Similarity	NPC599943
0.5254	Remote Similarity	NPC78809
0.5254	Remote Similarity	NPC190217
0.5254	Remote Similarity	NPC469661
0.5254	Remote Similarity	NPC65530
0.5254	Remote Similarity	NPC611586
0.5246	Remote Similarity	NPC98777
0.5246	Remote Similarity	NPC189115
0.5246	Remote Similarity	NPC212770
0.5238	Remote Similarity	NPC186406
0.5238	Remote Similarity	NPC299435
0.5238	Remote Similarity	NPC169248
0.5238	Remote Similarity	NPC72649
0.5231	Remote Similarity	NPC206378
0.5231	Remote Similarity	NPC106625
0.5185	Remote Similarity	NPC9912
0.5172	Remote Similarity	NPC287872
0.5172	Remote Similarity	NPC247146
0.5167	Remote Similarity	NPC111536
0.5167	Remote Similarity	NPC186418
0.5167	Remote Similarity	NPC479374
0.5167	Remote Similarity	NPC604095
0.5161	Remote Similarity	NPC78697
0.5156	Remote Similarity	NPC328093
0.5156	Remote Similarity	NPC259182
0.5156	Remote Similarity	NPC88484
0.5156	Remote Similarity	NPC185103
0.5152	Remote Similarity	NPC145319
0.5094	Remote Similarity	NPC69513
0.5088	Remote Similarity	NPC609351
0.5085	Remote Similarity	NPC100389
0.5085	Remote Similarity	NPC190714
0.5085	Remote Similarity	NPC99515
0.5085	Remote Similarity	NPC605646
0.5082	Remote Similarity	NPC604892
0.5079	Remote Similarity	NPC606353
0.5077	Remote Similarity	NPC471457
0.5077	Remote Similarity	NPC260604
0.5077	Remote Similarity	NPC26195
0.5075	Remote Similarity	NPC287294
0.5075	Remote Similarity	NPC143851

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC612000 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5224
0.1-0.2	3734
0.2-0.3	157
0.3-0.4	28
0.4-0.5	5
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
0.549	Remote Similarity	NPD1091	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