NPASS Compound

Natural Product: NPC604218

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 44 43 0 0 0 0 0 0 0 0999 V2000 -4.3298 -1.6877 -1.1916 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1449 -1.0987 -0.0832 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3047 -0.0724 0.6679 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9064 0.9896 -0.3181 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0710 2.0815 0.2722 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7824 1.5529 0.8544 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9653 0.8732 -0.2206 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3408 0.3337 0.3333 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0980 -0.3283 -0.7966 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4121 -0.8982 -0.3516 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3346 0.1610 0.2182 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6277 -0.4438 0.6476 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4013 -1.1195 -0.4314 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7792 -0.2344 -1.5437 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4357 -0.7377 -2.4927 O 0 0 0 0 0 0 0 0 0 0 0 0 5.4731 1.1020 -1.6319 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3103 -1.0438 -2.0876 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3016 -1.9775 -0.8615 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8308 -2.6437 -1.5160 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0064 -0.5551 -0.5190 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4872 -1.9077 0.5987 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4660 -0.5873 1.1510 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9459 0.3868 1.4548 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3855 0.5275 -1.1719 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8713 1.3899 -0.7410 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6243 2.7107 0.9910 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8117 2.7772 -0.5771 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2093 2.3337 1.3846 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0538 0.7954 1.6154 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5056 -0.0041 -0.6283 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7752 1.5687 -1.0611 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1564 -0.4154 1.1031 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9574 1.1961 0.6729 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1978 0.3780 -1.6524 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4816 -1.1731 -1.1675 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1906 -1.6886 0.3940 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8887 -1.3829 -1.2109 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4120 1.0413 -0.4229 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8246 0.5175 1.1633 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4005 -1.2081 1.4269 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2770 0.3059 1.1258 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8754 -2.0496 -0.7994 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3425 -1.4957 0.0254 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1824 1.7306 -2.0142 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 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 2 0 14 16 1 0 1 17 1 0 1 18 1 0 1 19 1 0 2 20 1 0 2 21 1 0 3 22 1 0 3 23 1 0 4 24 1 0 4 25 1 0 5 26 1 0 5 27 1 0 6 28 1 0 6 29 1 0 7 30 1 0 7 31 1 0 8 32 1 0 8 33 1 0 9 34 1 0 9 35 1 0 10 36 1 0 10 37 1 0 11 38 1 0 11 39 1 0 12 40 1 0 12 41 1 0 13 42 1 0 13 43 1 0 16 44 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 NPC604218 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	39487
0.1-0.2	8829
0.2-0.3	1101
0.3-0.4	238
0.4-0.5	86
0.5-0.6	42
0.6-0.7	14
0.7-0.8	3
0.8-0.85	2
0.85-0.9	4
0.9-0.95	0
0.95-1	16

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC171736
1.0	High Similarity	NPC301585
1.0	High Similarity	NPC261080
1.0	High Similarity	NPC132565
1.0	High Similarity	NPC209970
1.0	High Similarity	NPC216630
1.0	High Similarity	NPC201844
1.0	High Similarity	NPC301696
1.0	High Similarity	NPC196924
1.0	High Similarity	NPC307783
1.0	High Similarity	NPC154186
1.0	High Similarity	NPC149184
1.0	High Similarity	NPC279026
1.0	High Similarity	NPC113928
1.0	High Similarity	NPC14227
0.95	High Similarity	NPC155263
0.85	High Similarity	NPC214610
0.85	High Similarity	NPC118968
0.85	High Similarity	NPC183424
0.85	High Similarity	NPC294085
0.8095	Intermediate Similarity	NPC175342
0.8	Intermediate Similarity	NPC268826
0.7692	Intermediate Similarity	NPC424
0.7692	Intermediate Similarity	NPC36061
0.7692	Intermediate Similarity	NPC69510
0.7692	Intermediate Similarity	NPC77272
0.7692	Intermediate Similarity	NPC8219
0.7692	Intermediate Similarity	NPC290563
0.7692	Intermediate Similarity	NPC139029
0.7692	Intermediate Similarity	NPC281972
0.7692	Intermediate Similarity	NPC261831
0.7692	Intermediate Similarity	NPC87564
0.75	Intermediate Similarity	NPC174368
0.7407	Intermediate Similarity	NPC18712
0.7407	Intermediate Similarity	NPC74845
0.7407	Intermediate Similarity	NPC95145
0.7407	Intermediate Similarity	NPC325642
0.7407	Intermediate Similarity	NPC65174
0.7308	Intermediate Similarity	NPC281245
0.72	Intermediate Similarity	NPC55023
0.72	Intermediate Similarity	NPC21844
0.7143	Intermediate Similarity	NPC134782
0.7143	Intermediate Similarity	NPC87394
0.7143	Intermediate Similarity	NPC324004
0.7143	Intermediate Similarity	NPC328497
0.7143	Intermediate Similarity	NPC602547
0.7083	Intermediate Similarity	NPC604140
0.7037	Intermediate Similarity	NPC129972
0.7037	Intermediate Similarity	NPC301528
0.7037	Intermediate Similarity	NPC71317
0.7037	Intermediate Similarity	NPC92114
0.7037	Intermediate Similarity	NPC163746
0.7037	Intermediate Similarity	NPC103286
0.6897	Remote Similarity	NPC154245
0.6897	Remote Similarity	NPC85813
0.6897	Remote Similarity	NPC223697
0.6897	Remote Similarity	NPC6095
0.6667	Remote Similarity	NPC314679
0.6552	Remote Similarity	NPC321062
0.6538	Remote Similarity	NPC180534
0.6538	Remote Similarity	NPC611531
0.6452	Remote Similarity	NPC40082
0.6296	Remote Similarity	NPC50457
0.6296	Remote Similarity	NPC604910
0.619	Remote Similarity	NPC18224
0.6071	Remote Similarity	NPC34416
0.6	Remote Similarity	NPC5413
0.5806	Remote Similarity	NPC52955
0.5806	Remote Similarity	NPC88966
0.5806	Remote Similarity	NPC25417
0.5806	Remote Similarity	NPC1813
0.5806	Remote Similarity	NPC59051
0.5714	Remote Similarity	NPC149209
0.5714	Remote Similarity	NPC106851
0.5714	Remote Similarity	NPC282788
0.5714	Remote Similarity	NPC274927
0.5714	Remote Similarity	NPC477201
0.5667	Remote Similarity	NPC73245
0.5556	Remote Similarity	NPC323974
0.5556	Remote Similarity	NPC317203
0.5556	Remote Similarity	NPC179764
0.5484	Remote Similarity	NPC158179
0.5484	Remote Similarity	NPC91495
0.5484	Remote Similarity	NPC70387
0.5405	Remote Similarity	NPC251042
0.5405	Remote Similarity	NPC318814
0.5405	Remote Similarity	NPC320669
0.5405	Remote Similarity	NPC243532
0.5405	Remote Similarity	NPC255863
0.5405	Remote Similarity	NPC99619
0.5405	Remote Similarity	NPC174447
0.5405	Remote Similarity	NPC136164
0.5405	Remote Similarity	NPC122521
0.5405	Remote Similarity	NPC245947
0.5405	Remote Similarity	NPC605064
0.5357	Remote Similarity	NPC602752
0.5312	Remote Similarity	NPC174560
0.5312	Remote Similarity	NPC125312
0.5263	Remote Similarity	NPC68343
0.5263	Remote Similarity	NPC318420
0.5263	Remote Similarity	NPC326268
0.5263	Remote Similarity	NPC328089
0.5172	Remote Similarity	NPC200618
0.5172	Remote Similarity	NPC131770
0.5172	Remote Similarity	NPC90904
0.5161	Remote Similarity	NPC149821
0.5143	Remote Similarity	NPC487561
0.5143	Remote Similarity	NPC225929
0.5143	Remote Similarity	NPC606120

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC604218 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6646
0.1-0.2	2113
0.2-0.3	287
0.3-0.4	70
0.4-0.5	16
0.5-0.6	4
0.6-0.7	4
0.7-0.8	3
0.8-0.85	0
0.85-0.9	1
0.9-0.95	0
0.95-1	3

Similarity Score	Similarity Level	Drug ID	Developmental Stage
1.0	High Similarity	NPD2270	Pre-clinical
1.0	High Similarity	NPD633	Phase 3
1.0	High Similarity	NPD9448	Phase 2
0.85	High Similarity	NPD9655	Phase 4
0.7692	Intermediate Similarity	NPD3195	Phase 2
0.7692	Intermediate Similarity	NPD3196	Approved
0.7143	Intermediate Similarity	NPD3199	Clinical (unspecified phase)
0.6897	Remote Similarity	NPD4266	Phase 2
0.6538	Remote Similarity	NPD622	Pre-clinical
0.6061	Remote Similarity	NPD3194	Phase 4
0.6	Remote Similarity	NPD3173	Phase 4
0.5806	Remote Similarity	NPD3172	Approved
0.5556	Remote Similarity	NPD3198	Phase 2
0.5556	Remote Similarity	NPD9019	Phase 4
0.5263	Remote Similarity	NPD39	Phase 4

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