NPASS Compound

Natural Product: NPC611531

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 39 38 0 0 0 0 0 0 0 0999 V2000 -6.0329 -0.9573 -1.4608 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7181 -0.8148 -1.5807 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8940 -0.0733 -0.5842 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8374 -0.9470 0.0344 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9793 -0.2686 1.0389 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2204 0.8997 0.4872 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3491 1.5922 1.4547 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7252 0.7264 2.0655 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6501 0.1450 1.0122 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3685 1.2116 0.2194 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2644 0.6033 -0.8261 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3187 -0.3115 -0.2546 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1206 -0.8248 -1.3797 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6866 -0.0093 -2.1481 O 0 0 0 0 0 0 0 0 0 0 0 0 5.2591 -2.1763 -1.6077 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.5095 -0.5007 -0.5814 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6131 -1.4958 -2.1917 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2456 -1.2617 -2.4474 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6014 0.2223 0.2360 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4921 0.8710 -0.9800 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2609 -1.4155 -0.7928 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3604 -1.8005 0.5363 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6345 0.1178 1.8510 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2421 -1.0073 1.4133 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9327 1.6599 0.0817 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6307 0.5446 -0.3837 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9224 2.0204 2.3083 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1542 2.4514 0.9684 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3322 -0.1197 2.6410 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3764 1.3099 2.7407 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1031 -0.5416 0.3409 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4560 -0.4277 1.5509 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9645 1.8334 0.9135 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6001 1.8194 -0.3094 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6570 0.0118 -1.5545 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7121 1.4400 -1.3985 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8416 -1.1596 0.2949 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9100 0.2706 0.4927 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9757 -2.5756 -2.2006 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 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 2 0 13 15 1 0 1 16 1 0 1 17 1 0 2 18 1 0 3 19 1 0 3 20 1 0 4 21 1 0 4 22 1 0 5 23 1 0 5 24 1 0 6 25 1 0 6 26 1 0 7 27 1 0 7 28 1 0 8 29 1 0 8 30 1 0 9 31 1 0 9 32 1 0 10 33 1 0 10 34 1 0 11 35 1 0 11 36 1 0 12 37 1 0 12 38 1 0 15 39 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 NPC611531 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	40936
0.1-0.2	7730
0.2-0.3	892
0.3-0.4	147
0.4-0.5	57
0.5-0.6	31
0.6-0.7	42
0.7-0.8	1
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	NPC180534
0.7391	Intermediate Similarity	NPC214610
0.7391	Intermediate Similarity	NPC118968
0.7391	Intermediate Similarity	NPC183424
0.7391	Intermediate Similarity	NPC294085
0.7143	Intermediate Similarity	NPC34416
0.7143	Intermediate Similarity	NPC281245
0.6957	Remote Similarity	NPC268826
0.6897	Remote Similarity	NPC424
0.6897	Remote Similarity	NPC36061
0.6897	Remote Similarity	NPC69510
0.6897	Remote Similarity	NPC77272
0.6897	Remote Similarity	NPC290563
0.6897	Remote Similarity	NPC139029
0.6897	Remote Similarity	NPC281972
0.6897	Remote Similarity	NPC261831
0.6897	Remote Similarity	NPC87564
0.6667	Remote Similarity	NPC95145
0.6667	Remote Similarity	NPC325642
0.6667	Remote Similarity	NPC65174
0.6538	Remote Similarity	NPC171736
0.6538	Remote Similarity	NPC301585
0.6538	Remote Similarity	NPC261080
0.6538	Remote Similarity	NPC132565
0.6538	Remote Similarity	NPC209970
0.6538	Remote Similarity	NPC216630
0.6538	Remote Similarity	NPC201844
0.6538	Remote Similarity	NPC301696
0.6538	Remote Similarity	NPC196924
0.6538	Remote Similarity	NPC307783
0.6538	Remote Similarity	NPC154186
0.6538	Remote Similarity	NPC149184
0.6538	Remote Similarity	NPC279026
0.6538	Remote Similarity	NPC113928
0.6538	Remote Similarity	NPC14227
0.6333	Remote Similarity	NPC92114
0.6296	Remote Similarity	NPC604140
0.625	Remote Similarity	NPC52955
0.625	Remote Similarity	NPC88966
0.625	Remote Similarity	NPC25417
0.625	Remote Similarity	NPC134782
0.625	Remote Similarity	NPC1813
0.625	Remote Similarity	NPC154245
0.625	Remote Similarity	NPC85813
0.625	Remote Similarity	NPC223697
0.625	Remote Similarity	NPC6095
0.6176	Remote Similarity	NPC18357
0.6154	Remote Similarity	NPC155263
0.6129	Remote Similarity	NPC207292
0.5938	Remote Similarity	NPC321062
0.5938	Remote Similarity	NPC70387
0.5862	Remote Similarity	NPC55023
0.5862	Remote Similarity	NPC21844
0.5769	Remote Similarity	NPC175342
0.5758	Remote Similarity	NPC174560
0.5758	Remote Similarity	NPC125312
0.5667	Remote Similarity	NPC50457
0.5667	Remote Similarity	NPC604910
0.5556	Remote Similarity	NPC225929
0.5556	Remote Similarity	NPC606120
0.5526	Remote Similarity	NPC485704
0.5484	Remote Similarity	NPC314679
0.5455	Remote Similarity	NPC5413
0.5455	Remote Similarity	NPC602547
0.5417	Remote Similarity	NPC18224
0.5312	Remote Similarity	NPC8219
0.5294	Remote Similarity	NPC59051
0.5263	Remote Similarity	NPC106851
0.5263	Remote Similarity	NPC282788
0.5263	Remote Similarity	NPC274927
0.5263	Remote Similarity	NPC477201
0.525	Remote Similarity	NPC68343
0.525	Remote Similarity	NPC54766
0.525	Remote Similarity	NPC328089
0.52	Remote Similarity	NPC174368
0.5152	Remote Similarity	NPC18712
0.5152	Remote Similarity	NPC149821
0.5152	Remote Similarity	NPC74845
0.5135	Remote Similarity	NPC487561
0.5128	Remote Similarity	NPC179764

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC611531 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7113
0.1-0.2	1763
0.2-0.3	216
0.3-0.4	37
0.4-0.5	8
0.5-0.6	2
0.6-0.7	7
0.7-0.8	1
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Drug ID	Developmental Stage
1.0	High Similarity	NPD622	Pre-clinical
0.7391	Intermediate Similarity	NPD9655	Phase 4
0.6897	Remote Similarity	NPD3195	Phase 2
0.6897	Remote Similarity	NPD3196	Approved
0.6538	Remote Similarity	NPD2270	Pre-clinical
0.6538	Remote Similarity	NPD633	Phase 3
0.6538	Remote Similarity	NPD9448	Phase 2
0.625	Remote Similarity	NPD3172	Approved
0.625	Remote Similarity	NPD4266	Phase 2
0.5556	Remote Similarity	NPD3194	Phase 4
0.5455	Remote Similarity	NPD3173	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