NPASS Compound

Natural Product: NPC610617

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 42 43 0 0 0 0 0 0 0 0999 V2000 2.8230 -2.6655 2.5708 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9034 -1.8934 1.8483 O 0 0 0 0 0 0 0 0 0 0 0 0 2.2697 -0.8424 1.0276 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5895 -0.4943 0.8763 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9743 0.5438 0.0680 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3883 0.9194 -0.0963 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9826 0.2312 -1.1577 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9894 1.2339 -0.5941 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6495 0.8773 -0.4380 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2470 -0.1484 0.3585 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0641 -0.5258 0.5346 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1347 0.0922 -0.0772 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.0423 0.4692 0.8859 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.1861 1.0405 0.4811 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.2567 0.7254 1.5390 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4758 1.2718 1.2134 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.7400 0.6925 -0.8436 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.2061 1.8515 -1.5101 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8191 -0.0028 -1.7778 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4909 -0.7092 -2.7719 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.8945 -0.8970 -0.9838 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.9953 -1.5675 -1.8128 O 0 0 0 0 0 0 0 0 0 0 0 0 3.5239 -3.1981 1.9016 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4325 -2.0456 3.2745 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2380 -3.4196 3.1624 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3690 -1.0390 1.3992 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4691 2.0110 -0.3357 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9649 0.6930 0.8464 H 0 0 0 0 0 0 0 0 0 0 0 0 6.9299 0.5161 -1.1827 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2898 2.0499 -1.2298 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9610 1.4876 -1.0051 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8703 0.9226 -0.7282 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0694 2.1617 0.5413 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3507 -0.3776 1.6341 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8635 1.1422 2.4928 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4128 1.9356 0.4901 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6629 0.0466 -0.7506 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7474 1.6068 -2.3012 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1666 0.7691 -2.2675 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8991 -0.7053 -3.5680 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5106 -1.5641 -0.3726 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1357 -1.6469 -1.3414 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 1 0 6 7 1 0 5 8 2 0 8 9 1 0 9 10 2 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 1 0 14 17 1 0 17 18 1 0 17 19 1 0 19 20 1 0 19 21 1 0 21 22 1 0 10 3 1 0 21 12 1 0 1 23 1 0 1 24 1 0 1 25 1 0 4 26 1 0 6 27 1 0 6 28 1 0 7 29 1 0 8 30 1 0 9 31 1 0 12 32 1 6 14 33 1 6 15 34 1 0 15 35 1 0 16 36 1 0 17 37 1 1 18 38 1 0 19 39 1 6 20 40 1 0 21 41 1 1 22 42 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 NPC610617 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	14632
0.1-0.2	30356
0.2-0.3	3821
0.3-0.4	665
0.4-0.5	277
0.5-0.6	77
0.6-0.7	15
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	NPC166040
0.7347	Intermediate Similarity	NPC299144
0.717	Intermediate Similarity	NPC472024
0.717	Intermediate Similarity	NPC270849
0.7083	Intermediate Similarity	NPC269242
0.7037	Intermediate Similarity	NPC26653
0.7037	Intermediate Similarity	NPC80600
0.6909	Remote Similarity	NPC248355
0.6786	Remote Similarity	NPC55040
0.6739	Remote Similarity	NPC228907
0.6667	Remote Similarity	NPC302378
0.6481	Remote Similarity	NPC9912
0.6471	Remote Similarity	NPC25817
0.6441	Remote Similarity	NPC276753
0.6441	Remote Similarity	NPC205796
0.6333	Remote Similarity	NPC37468
0.6333	Remote Similarity	NPC246947
0.6333	Remote Similarity	NPC604095
0.6316	Remote Similarity	NPC479029
0.6226	Remote Similarity	NPC226712
0.619	Remote Similarity	NPC25821
0.6129	Remote Similarity	NPC111785
0.5965	Remote Similarity	NPC479028
0.5965	Remote Similarity	NPC479031
0.5962	Remote Similarity	NPC153149
0.5882	Remote Similarity	NPC276195
0.5882	Remote Similarity	NPC212729
0.5882	Remote Similarity	NPC604498
0.5818	Remote Similarity	NPC69513
0.5769	Remote Similarity	NPC217854
0.5758	Remote Similarity	NPC158635
0.5758	Remote Similarity	NPC229882
0.5741	Remote Similarity	NPC609376
0.5714	Remote Similarity	NPC48863
0.5714	Remote Similarity	NPC251981
0.5714	Remote Similarity	NPC13745
0.5672	Remote Similarity	NPC327032
0.5672	Remote Similarity	NPC286235
0.566	Remote Similarity	NPC294470
0.5636	Remote Similarity	NPC608788
0.5614	Remote Similarity	NPC215833
0.5593	Remote Similarity	NPC210478
0.5588	Remote Similarity	NPC38041
0.5588	Remote Similarity	NPC227902
0.5588	Remote Similarity	NPC18979
0.5588	Remote Similarity	NPC22150
0.5588	Remote Similarity	NPC279298
0.5556	Remote Similarity	NPC152722
0.5536	Remote Similarity	NPC145900
0.5517	Remote Similarity	NPC218685
0.5517	Remote Similarity	NPC49074
0.5507	Remote Similarity	NPC471063
0.5455	Remote Similarity	NPC60589
0.5455	Remote Similarity	NPC469708
0.5455	Remote Similarity	NPC605700
0.5439	Remote Similarity	NPC166168
0.5424	Remote Similarity	NPC162093
0.541	Remote Similarity	NPC104167
0.5397	Remote Similarity	NPC294166
0.5397	Remote Similarity	NPC115022
0.537	Remote Similarity	NPC192810
0.5357	Remote Similarity	NPC200092
0.5345	Remote Similarity	NPC40377
0.5323	Remote Similarity	NPC247146
0.5312	Remote Similarity	NPC479030
0.5312	Remote Similarity	NPC610808
0.5294	Remote Similarity	NPC160780
0.5294	Remote Similarity	NPC606202
0.5283	Remote Similarity	NPC142319
0.5278	Remote Similarity	NPC93924
0.5278	Remote Similarity	NPC217635
0.5263	Remote Similarity	NPC221090
0.5263	Remote Similarity	NPC80098
0.5224	Remote Similarity	NPC148273
0.5217	Remote Similarity	NPC61594
0.5205	Remote Similarity	NPC43508
0.5172	Remote Similarity	NPC95292
0.5167	Remote Similarity	NPC205054
0.5167	Remote Similarity	NPC23084
0.5167	Remote Similarity	NPC604356
0.5161	Remote Similarity	NPC95392
0.5161	Remote Similarity	NPC84013
0.5161	Remote Similarity	NPC55715
0.5161	Remote Similarity	NPC35877
0.5152	Remote Similarity	NPC210192
0.5152	Remote Similarity	NPC475096
0.5152	Remote Similarity	NPC475084
0.5143	Remote Similarity	NPC56735
0.5135	Remote Similarity	NPC299706
0.5135	Remote Similarity	NPC245615
0.5135	Remote Similarity	NPC186316
0.5135	Remote Similarity	NPC115466
0.5135	Remote Similarity	NPC39657
0.5135	Remote Similarity	NPC61604
0.5088	Remote Similarity	NPC12308
0.5085	Remote Similarity	NPC310661
0.5079	Remote Similarity	NPC232673
0.5077	Remote Similarity	NPC486107
0.5072	Remote Similarity	NPC212099

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC610617 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4069
0.1-0.2	4864
0.2-0.3	195
0.3-0.4	18
0.4-0.5	3
0.5-0.6	0
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
0.6226	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