NPASS Compound

Natural Product: NPC603056

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 33 35 0 0 0 0 0 0 0 0999 V2000 6.2328 -0.2108 -0.7393 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3609 0.7666 -0.2473 O 0 0 0 0 0 0 0 0 0 0 0 0 4.0113 0.4707 -0.1051 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4745 -0.7495 -0.4259 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1176 -1.0305 -0.2773 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2620 -0.0642 0.2080 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1692 -0.3331 0.3743 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6190 -1.5161 0.9524 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9052 -1.7659 1.1057 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8459 -0.9339 0.7321 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1966 -1.2288 0.9087 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1821 -0.3480 0.5130 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5291 -0.6369 0.6866 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.8058 0.8440 -0.0675 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4674 1.1297 -0.2394 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0752 2.3272 -0.8229 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4604 0.2519 0.1544 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1261 0.5585 -0.0274 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8184 1.6499 -0.5579 O 0 0 0 0 0 0 0 0 0 0 0 0 1.8027 1.1640 0.5310 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1393 1.4410 0.3845 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3975 -0.9663 0.0723 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2030 0.2495 -1.0302 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8220 -0.6845 -1.6431 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1491 -1.5044 -0.8062 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7585 -2.0095 -0.5476 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1151 -2.2530 1.2859 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4477 -2.1697 1.3657 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9220 -1.5507 0.7111 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5664 1.5594 -0.3900 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4113 3.2358 -0.5187 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1229 1.9132 0.9102 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5787 2.3942 0.6316 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 3 1 0 18 7 1 0 17 10 1 0 1 22 1 0 1 23 1 0 1 24 1 0 4 25 1 0 5 26 1 0 8 27 1 0 11 28 1 0 13 29 1 0 14 30 1 0 16 31 1 0 20 32 1 0 21 33 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 NPC603056 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	26568
0.1-0.2	19657
0.2-0.3	2717
0.3-0.4	624
0.4-0.5	191
0.5-0.6	56
0.6-0.7	30
0.7-0.8	1
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC294409
1.0	High Similarity	NPC490701
0.8113	Intermediate Similarity	NPC200316
0.7963	Intermediate Similarity	NPC194653
0.7636	Intermediate Similarity	NPC279668
0.7636	Intermediate Similarity	NPC278323
0.7547	Intermediate Similarity	NPC78341
0.7255	Intermediate Similarity	NPC39426
0.7255	Intermediate Similarity	NPC608554
0.7222	Intermediate Similarity	NPC116632
0.7222	Intermediate Similarity	NPC35763
0.7193	Intermediate Similarity	NPC254702
0.7069	Intermediate Similarity	NPC104728
0.7049	Intermediate Similarity	NPC233918
0.7018	Intermediate Similarity	NPC481044
0.6964	Remote Similarity	NPC239363
0.6935	Remote Similarity	NPC479305
0.6897	Remote Similarity	NPC142876
0.6842	Remote Similarity	NPC309154
0.6786	Remote Similarity	NPC209560
0.6786	Remote Similarity	NPC490700
0.6731	Remote Similarity	NPC193792
0.6667	Remote Similarity	NPC19980
0.6667	Remote Similarity	NPC38065
0.661	Remote Similarity	NPC483637
0.661	Remote Similarity	NPC264550
0.6471	Remote Similarity	NPC156457
0.6462	Remote Similarity	NPC107838
0.6349	Remote Similarity	NPC133400
0.6333	Remote Similarity	NPC45291
0.6316	Remote Similarity	NPC10467
0.625	Remote Similarity	NPC268059
0.6207	Remote Similarity	NPC124714
0.6207	Remote Similarity	NPC303644
0.6207	Remote Similarity	NPC121522
0.6154	Remote Similarity	NPC128774
0.6129	Remote Similarity	NPC167595
0.6094	Remote Similarity	NPC249824
0.6094	Remote Similarity	NPC40942
0.6071	Remote Similarity	NPC87545
0.6061	Remote Similarity	NPC476178
0.6061	Remote Similarity	NPC474052
0.6034	Remote Similarity	NPC131266
0.6034	Remote Similarity	NPC269451
0.6034	Remote Similarity	NPC603503
0.597	Remote Similarity	NPC482075
0.5833	Remote Similarity	NPC209487
0.5781	Remote Similarity	NPC203636
0.5781	Remote Similarity	NPC608523
0.5763	Remote Similarity	NPC59951
0.5763	Remote Similarity	NPC231772
0.5763	Remote Similarity	NPC241838
0.5735	Remote Similarity	NPC231763
0.5735	Remote Similarity	NPC74178
0.5692	Remote Similarity	NPC213659
0.5692	Remote Similarity	NPC326109
0.5672	Remote Similarity	NPC280937
0.5667	Remote Similarity	NPC69430
0.5614	Remote Similarity	NPC182428
0.5614	Remote Similarity	NPC120924
0.5538	Remote Similarity	NPC238279
0.5522	Remote Similarity	NPC475705
0.5517	Remote Similarity	NPC223354
0.5507	Remote Similarity	NPC303197
0.5507	Remote Similarity	NPC600495
0.55	Remote Similarity	NPC7013
0.55	Remote Similarity	NPC333691
0.5484	Remote Similarity	NPC12377
0.5429	Remote Similarity	NPC52889
0.541	Remote Similarity	NPC181124
0.541	Remote Similarity	NPC245382
0.541	Remote Similarity	NPC216769
0.541	Remote Similarity	NPC610981
0.5405	Remote Similarity	NPC138540
0.5397	Remote Similarity	NPC80710
0.5397	Remote Similarity	NPC90665
0.5373	Remote Similarity	NPC606200
0.5362	Remote Similarity	NPC488570
0.5333	Remote Similarity	NPC481043
0.5333	Remote Similarity	NPC474264
0.5312	Remote Similarity	NPC55162
0.5312	Remote Similarity	NPC476055
0.5312	Remote Similarity	NPC114192
0.5246	Remote Similarity	NPC474340
0.5224	Remote Similarity	NPC85131
0.5224	Remote Similarity	NPC232947
0.5161	Remote Similarity	NPC186507
0.5161	Remote Similarity	NPC162680
0.5161	Remote Similarity	NPC136095
0.5161	Remote Similarity	NPC100971
0.5161	Remote Similarity	NPC609386
0.5156	Remote Similarity	NPC12175
0.5152	Remote Similarity	NPC93552
0.5143	Remote Similarity	NPC149875
0.5139	Remote Similarity	NPC474960
0.5125	Remote Similarity	NPC121647
0.5082	Remote Similarity	NPC605229
0.5079	Remote Similarity	NPC181209
0.5079	Remote Similarity	NPC250557
0.5079	Remote Similarity	NPC605826
0.5067	Remote Similarity	NPC73511

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC603056 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4559
0.1-0.2	4465
0.2-0.3	115
0.3-0.4	8
0.4-0.5	2
0.5-0.6	0
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
0.7255	Intermediate 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