NPASS Compound

Natural Product: NPC602262

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 -5.8448 0.3068 1.1464 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2267 -0.0113 -0.0715 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.8566 0.0463 -0.2273 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0857 0.4258 0.8424 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6937 0.4944 0.7172 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0613 0.1872 -0.4681 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3810 0.2610 -0.5884 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9686 0.8594 -1.6977 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2708 0.9136 -1.7830 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0650 0.4246 -0.8611 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4470 0.5170 -1.0168 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2513 -0.0092 -0.0253 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6162 0.0657 -0.1485 O 0 0 0 0 0 0 0 0 0 0 0 0 4.7298 -0.6155 1.0995 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3612 -0.7009 1.2423 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7584 -1.2939 2.3414 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5294 -0.1836 0.2672 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1592 -0.2728 0.4171 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6424 -0.8263 1.4434 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.8586 -0.1911 -1.5272 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2523 -0.2658 -1.4220 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0385 -0.6510 -2.5068 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.4769 1.2969 1.5350 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9499 0.3047 1.0763 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5820 -0.4818 1.9022 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5520 0.6762 1.7962 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1627 0.8016 1.6071 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2923 1.2554 -2.4447 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8538 0.9944 -1.9025 H 0 0 0 0 0 0 0 0 0 0 0 0 7.0758 0.7016 -0.8078 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3522 -1.0301 1.8806 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1090 -2.2216 2.5949 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4501 -0.4508 -2.4970 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7715 -1.3268 -2.3356 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 2 0 6 7 1 0 7 8 2 0 8 9 1 0 9 10 1 0 10 11 2 0 11 12 1 0 12 13 1 0 12 14 2 0 14 15 1 0 15 16 1 0 15 17 2 0 17 18 1 0 18 19 2 0 6 20 1 0 20 21 2 0 21 22 1 0 21 3 1 0 18 7 1 0 17 10 1 0 1 23 1 0 1 24 1 0 1 25 1 0 4 26 1 0 5 27 1 0 8 28 1 0 11 29 1 0 13 30 1 0 14 31 1 0 16 32 1 0 20 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 NPC602262 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	27392
0.1-0.2	19083
0.2-0.3	2499
0.3-0.4	641
0.4-0.5	160
0.5-0.6	48
0.6-0.7	21
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	NPC194653
0.7963	Intermediate Similarity	NPC294409
0.7963	Intermediate Similarity	NPC490701
0.7679	Intermediate Similarity	NPC200316
0.7544	Intermediate Similarity	NPC481044
0.75	Intermediate Similarity	NPC209487
0.7414	Intermediate Similarity	NPC254702
0.7143	Intermediate Similarity	NPC78341
0.7119	Intermediate Similarity	NPC142876
0.6949	Remote Similarity	NPC80710
0.6909	Remote Similarity	NPC38065
0.6897	Remote Similarity	NPC19980
0.6833	Remote Similarity	NPC45291
0.6721	Remote Similarity	NPC104728
0.6719	Remote Similarity	NPC233918
0.6667	Remote Similarity	NPC279668
0.6667	Remote Similarity	NPC278323
0.6667	Remote Similarity	NPC193792
0.6615	Remote Similarity	NPC479305
0.6615	Remote Similarity	NPC128774
0.661	Remote Similarity	NPC181209
0.661	Remote Similarity	NPC239363
0.6557	Remote Similarity	NPC483637
0.6557	Remote Similarity	NPC264550
0.6545	Remote Similarity	NPC39426
0.6545	Remote Similarity	NPC608554
0.65	Remote Similarity	NPC309154
0.6418	Remote Similarity	NPC482075
0.6029	Remote Similarity	NPC604255
0.6	Remote Similarity	NPC35763
0.597	Remote Similarity	NPC268059
0.5968	Remote Similarity	NPC264289
0.5942	Remote Similarity	NPC74178
0.5942	Remote Similarity	NPC107838
0.5902	Remote Similarity	NPC245382
0.5857	Remote Similarity	NPC52889
0.5857	Remote Similarity	NPC611367
0.5846	Remote Similarity	NPC167595
0.5806	Remote Similarity	NPC82325
0.5806	Remote Similarity	NPC54394
0.5763	Remote Similarity	NPC87545
0.5738	Remote Similarity	NPC116632
0.5738	Remote Similarity	NPC131266
0.5738	Remote Similarity	NPC269451
0.5714	Remote Similarity	NPC139293
0.5714	Remote Similarity	NPC52005
0.5571	Remote Similarity	NPC474052
0.5556	Remote Similarity	NPC184755
0.5556	Remote Similarity	NPC250557
0.5541	Remote Similarity	NPC156457
0.5526	Remote Similarity	NPC488441
0.5522	Remote Similarity	NPC238279
0.5441	Remote Similarity	NPC213659
0.5441	Remote Similarity	NPC326109
0.5429	Remote Similarity	NPC280937
0.5397	Remote Similarity	NPC303644
0.5397	Remote Similarity	NPC121522
0.5397	Remote Similarity	NPC209560
0.5397	Remote Similarity	NPC490700
0.5362	Remote Similarity	NPC606200
0.5325	Remote Similarity	NPC349624
0.5303	Remote Similarity	NPC114192
0.5294	Remote Similarity	NPC608523
0.5286	Remote Similarity	NPC475705
0.5278	Remote Similarity	NPC231763
0.5238	Remote Similarity	NPC603503
0.5231	Remote Similarity	NPC12377
0.5156	Remote Similarity	NPC124714
0.5156	Remote Similarity	NPC100971
0.5152	Remote Similarity	NPC139364
0.5143	Remote Similarity	NPC249824
0.5143	Remote Similarity	NPC133400
0.5135	Remote Similarity	NPC474960
0.5128	Remote Similarity	NPC481043
0.5077	Remote Similarity	NPC605826
0.5075	Remote Similarity	NPC109187
0.5075	Remote Similarity	NPC476055
0.5068	Remote Similarity	NPC303197

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC602262 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4966
0.1-0.2	4108
0.2-0.3	68
0.3-0.4	7
0.4-0.5	0
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
0.6545	Remote Similarity	NPD1510	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