NPASS Compound

Natural Product: NPC601132

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 46 48 0 0 0 0 0 0 0 0999 V2000 5.1152 1.1471 -2.8512 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5392 1.6206 -1.6517 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3483 1.1388 -1.1263 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6274 0.1481 -1.7585 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4628 -0.3176 -1.2373 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9807 0.2047 -0.0503 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7173 1.2079 0.5833 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8988 1.6911 0.0711 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6745 2.6789 0.6485 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3700 3.3516 1.8508 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2904 -0.2775 0.5358 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4666 0.6176 0.1293 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7296 0.1286 0.6993 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1816 0.5318 1.9280 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3792 0.0539 2.4636 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1368 -0.8436 1.7557 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3284 -1.3200 2.2896 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.7007 -1.2570 0.5265 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5169 -0.7803 0.0032 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5960 -1.6038 0.1768 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.9962 -2.4398 1.2932 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2051 -2.2815 -0.7692 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6702 -1.4171 -1.9253 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4727 1.5116 -3.7031 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1129 1.5942 -3.0340 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1486 0.0442 -2.8994 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9969 -0.2710 -2.6929 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3552 1.6385 1.5275 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7897 4.3793 1.8748 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8327 2.8206 2.7232 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2976 3.4129 2.0319 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2090 -0.2613 1.6722 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2037 1.6470 0.4912 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5461 0.7008 -0.9703 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6480 1.2233 2.5315 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7188 0.3788 3.4238 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0457 -0.7393 2.6920 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3176 -1.9752 -0.0244 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2030 -1.1248 -0.9670 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1281 -1.8897 2.2219 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9207 -2.9710 0.9905 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2088 -3.2409 1.3888 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0613 -2.7597 -0.2477 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3762 -3.1124 -1.2147 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2050 -1.0110 -2.4286 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3758 -1.9777 -2.5492 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 6 11 1 0 11 12 1 0 12 13 1 0 13 14 2 0 14 15 1 0 15 16 2 0 16 17 1 0 16 18 1 0 18 19 2 0 11 20 1 0 20 21 1 0 20 22 1 0 22 23 1 0 8 3 1 0 19 13 1 0 23 5 1 0 1 24 1 0 1 25 1 0 1 26 1 0 4 27 1 0 7 28 1 0 10 29 1 0 10 30 1 0 10 31 1 0 11 32 1 0 12 33 1 0 12 34 1 0 14 35 1 0 15 36 1 0 17 37 1 0 18 38 1 0 19 39 1 0 21 40 1 0 21 41 1 0 21 42 1 0 22 43 1 0 22 44 1 0 23 45 1 0 23 46 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 NPC601132 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	27623
0.1-0.2	18790
0.2-0.3	2983
0.3-0.4	243
0.4-0.5	131
0.5-0.6	55
0.6-0.7	9
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	NPC185838
0.7692	Intermediate Similarity	NPC191376
0.7551	Intermediate Similarity	NPC314682
0.7547	Intermediate Similarity	NPC321505
0.7547	Intermediate Similarity	NPC179825
0.7222	Intermediate Similarity	NPC135538
0.7222	Intermediate Similarity	NPC24233
0.7119	Intermediate Similarity	NPC317272
0.7119	Intermediate Similarity	NPC268503
0.7059	Intermediate Similarity	NPC213206
0.7059	Intermediate Similarity	NPC188163
0.7059	Intermediate Similarity	NPC328750
0.6774	Remote Similarity	NPC256012
0.6774	Remote Similarity	NPC610965
0.6615	Remote Similarity	NPC610959
0.6515	Remote Similarity	NPC480591
0.6429	Remote Similarity	NPC103379
0.6364	Remote Similarity	NPC240841
0.6346	Remote Similarity	NPC484289
0.6271	Remote Similarity	NPC247639
0.6271	Remote Similarity	NPC25084
0.597	Remote Similarity	NPC603603
0.5862	Remote Similarity	NPC147390
0.5862	Remote Similarity	NPC428
0.5775	Remote Similarity	NPC600054
0.5775	Remote Similarity	NPC601504
0.5694	Remote Similarity	NPC601503
0.5634	Remote Similarity	NPC609914
0.5479	Remote Similarity	NPC185639
0.5479	Remote Similarity	NPC251735
0.5479	Remote Similarity	NPC49075
0.5479	Remote Similarity	NPC223690
0.5479	Remote Similarity	NPC9532
0.5479	Remote Similarity	NPC599951
0.5441	Remote Similarity	NPC480592
0.5424	Remote Similarity	NPC609731
0.541	Remote Similarity	NPC39701
0.541	Remote Similarity	NPC184026
0.5405	Remote Similarity	NPC274716
0.5405	Remote Similarity	NPC167116
0.5405	Remote Similarity	NPC609821
0.5333	Remote Similarity	NPC181796
0.5333	Remote Similarity	NPC290005
0.5333	Remote Similarity	NPC54654
0.5333	Remote Similarity	NPC7715
0.5333	Remote Similarity	NPC328155
0.5333	Remote Similarity	NPC222661
0.5333	Remote Similarity	NPC285931
0.5323	Remote Similarity	NPC469817
0.5278	Remote Similarity	NPC290582
0.5278	Remote Similarity	NPC217748
0.5278	Remote Similarity	NPC182052
0.5278	Remote Similarity	NPC271013
0.5278	Remote Similarity	NPC42663
0.5278	Remote Similarity	NPC15414
0.5238	Remote Similarity	NPC27887
0.5205	Remote Similarity	NPC279228
0.5195	Remote Similarity	NPC212237
0.5195	Remote Similarity	NPC601489
0.5195	Remote Similarity	NPC604804
0.5143	Remote Similarity	NPC276890
0.5135	Remote Similarity	NPC311973
0.5135	Remote Similarity	NPC239824
0.5135	Remote Similarity	NPC112248
0.5135	Remote Similarity	NPC600872
0.5128	Remote Similarity	NPC24260
0.5128	Remote Similarity	NPC605743
0.5128	Remote Similarity	NPC611658
0.5079	Remote Similarity	NPC276588
0.5079	Remote Similarity	NPC127674
0.5079	Remote Similarity	NPC278799
0.5077	Remote Similarity	NPC474931
0.5067	Remote Similarity	NPC254441
0.5067	Remote Similarity	NPC116465
0.5065	Remote Similarity	NPC16357
0.5065	Remote Similarity	NPC302245

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC601132 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4221
0.1-0.2	4599
0.2-0.3	294
0.3-0.4	26
0.4-0.5	6
0.5-0.6	1
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
0.7059	Intermediate Similarity	NPD4664	Clinical (unspecified phase)
0.5156	Remote Similarity	NPD4010	Discontinued

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