NPASS Compound

Natural Product: NPC545930

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 36 38 0 0 0 0 0 0 0 0999 V2000 -4.3516 -2.0126 -0.9261 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2371 -0.7288 -0.3769 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0724 0.0050 -0.3153 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7144 0.8536 -1.3344 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5009 1.0203 -2.4793 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5399 1.5816 -1.2524 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7040 1.4613 -0.1304 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4693 2.1825 -0.0385 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5065 1.8344 0.8812 C 0 0 2 0 0 0 0 0 0 0 0 0 2.3154 0.7054 0.3597 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6649 -0.3892 1.1080 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4331 -1.4351 0.5773 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8702 -1.4042 -0.7261 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6389 -2.4510 -1.2566 O 0 0 0 0 0 0 0 0 0 0 0 0 3.5243 -0.3092 -1.4863 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7711 0.7160 -0.9652 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8791 1.4954 2.2366 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1977 0.4882 2.0492 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3881 -0.4593 2.8501 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0622 0.6142 0.8860 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2536 -0.1120 0.7823 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5370 -0.9458 1.8591 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4009 -2.4829 -1.1940 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9963 -2.0326 -1.8424 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9125 -2.6330 -0.1736 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4069 1.4788 -2.4531 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2299 2.2663 -2.0514 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0934 2.7601 1.0461 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3306 -0.4445 2.1458 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6763 -2.2757 1.2248 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6329 -2.3780 -1.4099 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8695 -0.2862 -2.5135 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4986 1.5837 -1.5719 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3924 2.4301 2.6499 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6501 1.2337 2.9446 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7109 -1.9306 1.6833 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 4 6 1 0 6 7 2 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 2 0 11 12 1 0 12 13 2 0 13 14 1 0 13 15 1 0 15 16 2 0 9 17 1 0 17 18 1 0 18 19 2 0 18 20 1 0 20 21 2 0 21 22 1 0 21 3 1 0 20 7 1 0 16 10 1 0 1 23 1 0 1 24 1 0 1 25 1 0 5 26 1 0 6 27 1 0 9 28 1 1 11 29 1 0 12 30 1 0 14 31 1 0 15 32 1 0 16 33 1 0 17 34 1 0 17 35 1 0 22 36 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 NPC545930 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	25328
0.1-0.2	19510
0.2-0.3	4147
0.3-0.4	610
0.4-0.5	186
0.5-0.6	56
0.6-0.7	12
0.7-0.8	0
0.8-0.85	2
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	NPC606248
0.8125	Intermediate Similarity	NPC255106
0.8125	Intermediate Similarity	NPC235165
0.7843	Intermediate Similarity	NPC474836
0.6923	Remote Similarity	NPC475267
0.6731	Remote Similarity	NPC329203
0.6731	Remote Similarity	NPC324386
0.6731	Remote Similarity	NPC222342
0.6667	Remote Similarity	NPC32441
0.6667	Remote Similarity	NPC79943
0.6471	Remote Similarity	NPC225153
0.6471	Remote Similarity	NPC479876
0.6415	Remote Similarity	NPC300668
0.6078	Remote Similarity	NPC329225
0.6078	Remote Similarity	NPC147686
0.6	Remote Similarity	NPC210084
0.5862	Remote Similarity	NPC236637
0.5818	Remote Similarity	NPC274784
0.5818	Remote Similarity	NPC20709
0.5714	Remote Similarity	NPC485881
0.5714	Remote Similarity	NPC469764
0.5574	Remote Similarity	NPC69674
0.5517	Remote Similarity	NPC302950
0.5484	Remote Similarity	NPC470131
0.5484	Remote Similarity	NPC470133
0.5484	Remote Similarity	NPC220998
0.5484	Remote Similarity	NPC470135
0.5484	Remote Similarity	NPC470132
0.5455	Remote Similarity	NPC243083
0.5455	Remote Similarity	NPC13768
0.5455	Remote Similarity	NPC6407
0.5455	Remote Similarity	NPC287246
0.5455	Remote Similarity	NPC545184
0.5455	Remote Similarity	NPC603284
0.5439	Remote Similarity	NPC321011
0.5439	Remote Similarity	NPC294852
0.5439	Remote Similarity	NPC188679
0.5439	Remote Similarity	NPC486095
0.5397	Remote Similarity	NPC134171
0.5397	Remote Similarity	NPC486094
0.537	Remote Similarity	NPC265871
0.537	Remote Similarity	NPC205093
0.5357	Remote Similarity	NPC150648
0.5357	Remote Similarity	NPC312391
0.5357	Remote Similarity	NPC167624
0.5357	Remote Similarity	NPC166482
0.5345	Remote Similarity	NPC48208
0.5323	Remote Similarity	NPC477841
0.5273	Remote Similarity	NPC476480
0.5273	Remote Similarity	NPC188243
0.5273	Remote Similarity	NPC110228
0.5273	Remote Similarity	NPC84585
0.5263	Remote Similarity	NPC99597
0.5263	Remote Similarity	NPC480993
0.5263	Remote Similarity	NPC338131
0.5246	Remote Similarity	NPC169591
0.5246	Remote Similarity	NPC298223
0.5246	Remote Similarity	NPC604412
0.5238	Remote Similarity	NPC477840
0.5179	Remote Similarity	NPC295261
0.5179	Remote Similarity	NPC296490
0.5179	Remote Similarity	NPC204515
0.5088	Remote Similarity	NPC1612
0.5088	Remote Similarity	NPC183959
0.5088	Remote Similarity	NPC37392
0.5088	Remote Similarity	NPC162869
0.5085	Remote Similarity	NPC18727
0.5085	Remote Similarity	NPC310135
0.5085	Remote Similarity	NPC601395
0.5075	Remote Similarity	NPC611447
0.507	Remote Similarity	NPC601453
0.507	Remote Similarity	NPC605491

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC545930 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4203
0.1-0.2	4778
0.2-0.3	150
0.3-0.4	12
0.4-0.5	3
0.5-0.6	2
0.6-0.7	2
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
0.6667	Remote Similarity	NPD1552	Clinical (unspecified phase)
0.6078	Remote Similarity	NPD1549	Phase 2
0.5517	Remote Similarity	NPD1934	Phase 0
0.5455	Remote Similarity	NPD1550	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