NPASS Compound

Natural Product: NPC608014

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 34 36 0 0 0 0 0 0 0 0999 V2000 -5.8559 -0.1288 -0.1609 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8987 0.3263 0.7463 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.5472 0.0956 0.6782 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9764 -1.0042 1.2765 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7587 -1.9279 1.9774 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6078 -1.2304 1.2029 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7782 -0.3565 0.5258 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5119 -0.5451 0.4410 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3239 0.2721 -0.1979 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7698 -0.0237 -0.2401 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6910 0.7635 -0.8775 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0458 0.4601 -0.9006 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5051 -0.6705 -0.2654 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8719 -0.9883 -0.2814 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5895 -1.4715 0.3797 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2501 -1.1536 0.3913 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8039 1.3829 -0.8111 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5663 1.6435 -0.7587 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0395 2.6731 -1.3285 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3463 0.7423 -0.0724 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7248 0.9651 0.0049 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2161 2.0906 -0.6220 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.4272 -0.9811 0.2658 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5397 0.7441 -0.3744 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4551 -0.4508 -1.1338 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5944 -1.6000 2.4736 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1312 -2.0843 1.6623 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3714 1.6662 -1.3920 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7632 1.1019 -1.4150 H 0 0 0 0 0 0 0 0 0 0 0 0 7.5617 -0.2754 -0.4570 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9683 -2.3573 0.8744 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5254 -1.7893 0.9030 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4287 2.0828 -1.3472 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5181 2.0286 -1.5895 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 1 0 9 10 1 0 10 11 2 0 11 12 1 0 12 13 2 0 13 14 1 0 13 15 1 0 15 16 2 0 9 17 2 0 17 18 1 0 18 19 2 0 18 20 1 0 20 21 2 0 21 22 1 0 21 3 1 0 20 7 1 0 16 10 1 0 1 23 1 0 1 24 1 0 1 25 1 0 5 26 1 0 6 27 1 0 11 28 1 0 12 29 1 0 14 30 1 0 15 31 1 0 16 32 1 0 17 33 1 0 22 34 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 NPC608014 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	29388
0.1-0.2	16649
0.2-0.3	2657
0.3-0.4	766
0.4-0.5	266
0.5-0.6	96
0.6-0.7	16
0.7-0.8	1
0.8-0.85	3
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	NPC241498
0.82	Intermediate Similarity	NPC100887
0.8163	Intermediate Similarity	NPC293183
0.8	Intermediate Similarity	NPC156222
0.7885	Intermediate Similarity	NPC83508
0.7358	Intermediate Similarity	NPC256283
0.7308	Intermediate Similarity	NPC284552
0.7222	Intermediate Similarity	NPC255350
0.717	Intermediate Similarity	NPC120163
0.6981	Remote Similarity	NPC266960
0.6667	Remote Similarity	NPC275836
0.6557	Remote Similarity	NPC470402
0.6545	Remote Similarity	NPC198826
0.6545	Remote Similarity	NPC234133
0.6481	Remote Similarity	NPC607196
0.6429	Remote Similarity	NPC78913
0.6364	Remote Similarity	NPC301323
0.6364	Remote Similarity	NPC47815
0.6346	Remote Similarity	NPC50898
0.625	Remote Similarity	NPC231018
0.6226	Remote Similarity	NPC130230
0.619	Remote Similarity	NPC213622
0.6102	Remote Similarity	NPC183950
0.6071	Remote Similarity	NPC71334
0.6071	Remote Similarity	NPC98661
0.5965	Remote Similarity	NPC231772
0.5965	Remote Similarity	NPC250266
0.5965	Remote Similarity	NPC163524
0.5965	Remote Similarity	NPC601901
0.5938	Remote Similarity	NPC196179
0.5893	Remote Similarity	NPC226973
0.5882	Remote Similarity	NPC272064
0.5862	Remote Similarity	NPC159275
0.5862	Remote Similarity	NPC25270
0.5833	Remote Similarity	NPC47781
0.5789	Remote Similarity	NPC239128
0.5789	Remote Similarity	NPC609062
0.5775	Remote Similarity	NPC475942
0.569	Remote Similarity	NPC184136
0.569	Remote Similarity	NPC62536
0.569	Remote Similarity	NPC145379
0.5667	Remote Similarity	NPC52005
0.5614	Remote Similarity	NPC26227
0.5593	Remote Similarity	NPC312924
0.5588	Remote Similarity	NPC600972
0.5574	Remote Similarity	NPC610914
0.5556	Remote Similarity	NPC172262
0.5517	Remote Similarity	NPC203891
0.5517	Remote Similarity	NPC44079
0.5507	Remote Similarity	NPC290830
0.5507	Remote Similarity	NPC71061
0.5507	Remote Similarity	NPC72425
0.5507	Remote Similarity	NPC600396
0.5484	Remote Similarity	NPC284220
0.5469	Remote Similarity	NPC603717
0.5455	Remote Similarity	NPC12367
0.5424	Remote Similarity	NPC120464
0.5424	Remote Similarity	NPC266597
0.5424	Remote Similarity	NPC269451
0.5424	Remote Similarity	NPC483773
0.541	Remote Similarity	NPC4455
0.541	Remote Similarity	NPC160951
0.541	Remote Similarity	NPC12200
0.541	Remote Similarity	NPC115323
0.541	Remote Similarity	NPC606638
0.537	Remote Similarity	NPC55557
0.5357	Remote Similarity	NPC222713
0.5352	Remote Similarity	NPC215203
0.5345	Remote Similarity	NPC472438
0.5345	Remote Similarity	NPC75279
0.5345	Remote Similarity	NPC602963
0.5333	Remote Similarity	NPC108406
0.5333	Remote Similarity	NPC9609
0.5333	Remote Similarity	NPC162313
0.5333	Remote Similarity	NPC605047
0.5323	Remote Similarity	NPC137062
0.5312	Remote Similarity	NPC486096
0.5278	Remote Similarity	NPC93337
0.5278	Remote Similarity	NPC205026
0.5273	Remote Similarity	NPC216318
0.5263	Remote Similarity	NPC279121
0.5254	Remote Similarity	NPC274327
0.5254	Remote Similarity	NPC275722
0.5254	Remote Similarity	NPC127447
0.5254	Remote Similarity	NPC103342
0.5254	Remote Similarity	NPC29353
0.5254	Remote Similarity	NPC194281
0.5246	Remote Similarity	NPC115798
0.5246	Remote Similarity	NPC69394
0.5246	Remote Similarity	NPC280339
0.5246	Remote Similarity	NPC29841
0.5238	Remote Similarity	NPC67322
0.5231	Remote Similarity	NPC476185
0.5231	Remote Similarity	NPC110969
0.5224	Remote Similarity	NPC34089
0.5211	Remote Similarity	NPC194593
0.5205	Remote Similarity	NPC105025
0.5185	Remote Similarity	NPC472992
0.5185	Remote Similarity	NPC143903
0.5179	Remote Similarity	NPC22783
0.5179	Remote Similarity	NPC78540
0.5167	Remote Similarity	NPC18260
0.5167	Remote Similarity	NPC57030
0.5167	Remote Similarity	NPC188203
0.5167	Remote Similarity	NPC276409
0.5167	Remote Similarity	NPC604085
0.5161	Remote Similarity	NPC607642
0.5152	Remote Similarity	NPC189706
0.5152	Remote Similarity	NPC265932
0.5143	Remote Similarity	NPC601984
0.5143	Remote Similarity	NPC603508
0.5088	Remote Similarity	NPC275772
0.5088	Remote Similarity	NPC296197
0.5085	Remote Similarity	NPC131624
0.5082	Remote Similarity	NPC201136
0.5082	Remote Similarity	NPC603662
0.5082	Remote Similarity	NPC604569
0.5079	Remote Similarity	NPC227325
0.5079	Remote Similarity	NPC606105
0.5072	Remote Similarity	NPC602497
0.507	Remote Similarity	NPC303485

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC608014 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5565
0.1-0.2	3486
0.2-0.3	88
0.3-0.4	9
0.4-0.5	0
0.5-0.6	1
0.6-0.7	0
0.7-0.8	1
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
0.7222	Intermediate Similarity	NPD2801	Pre-clinical
0.5263	Remote Similarity	NPD1511	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