NPASS Compound

Natural Product: NPC603415

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 32 34 0 0 0 0 0 0 0 0999 V2000 -1.5803 2.6519 -0.7651 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0333 1.5816 -0.4227 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4402 1.5124 -0.3828 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8866 0.0562 -0.5482 C 0 0 1 0 0 0 0 0 0 0 0 0 2.3409 0.0298 -0.3194 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2351 -0.0772 -1.3428 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6055 -0.1025 -1.1342 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0620 -0.0156 0.1581 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1931 0.0946 1.2319 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8203 0.1155 0.9650 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1650 -0.7647 0.3293 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2046 -0.7464 0.3059 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9849 -1.8484 0.6418 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3597 -1.7384 0.5896 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1777 -2.8251 0.9202 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.9681 -0.5575 0.2111 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3654 -0.5055 0.1768 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2079 0.5424 -0.1244 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7700 1.7441 -0.5089 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.8415 0.4253 -0.0701 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7683 1.8591 0.6065 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9195 2.0727 -1.2132 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6879 -0.2730 -1.5956 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8764 -0.1444 -2.3437 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3065 -0.1864 -1.9366 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1328 -0.0336 0.3442 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5674 0.1607 2.2258 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1781 0.2014 1.8165 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5158 -2.7704 0.9373 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6010 -2.8065 1.8595 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8110 -0.2377 -0.6876 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7645 2.5855 0.0758 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 2 0 6 7 1 0 7 8 2 0 8 9 1 0 9 10 2 0 4 11 1 0 11 12 1 0 12 13 2 0 13 14 1 0 14 15 1 0 14 16 2 0 16 17 1 0 16 18 1 0 18 19 1 0 18 20 2 0 20 2 1 0 10 5 1 0 20 12 1 0 3 21 1 0 3 22 1 0 4 23 1 6 6 24 1 0 7 25 1 0 8 26 1 0 9 27 1 0 10 28 1 0 13 29 1 0 15 30 1 0 17 31 1 0 19 32 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 NPC603415 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	24917
0.1-0.2	21987
0.2-0.3	2409
0.3-0.4	367
0.4-0.5	120
0.5-0.6	38
0.6-0.7	11
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	NPC204515
0.6735	Remote Similarity	NPC243083
0.6735	Remote Similarity	NPC13768
0.6735	Remote Similarity	NPC287246
0.66	Remote Similarity	NPC312391
0.6471	Remote Similarity	NPC255106
0.6471	Remote Similarity	NPC482119
0.6471	Remote Similarity	NPC235165
0.6471	Remote Similarity	NPC482120
0.6275	Remote Similarity	NPC150648
0.6	Remote Similarity	NPC265871
0.6	Remote Similarity	NPC205093
0.5965	Remote Similarity	NPC39045
0.5962	Remote Similarity	NPC37392
0.5882	Remote Similarity	NPC476480
0.5882	Remote Similarity	NPC84585
0.5849	Remote Similarity	NPC194432
0.569	Remote Similarity	NPC1089
0.5577	Remote Similarity	NPC213322
0.5556	Remote Similarity	NPC99597
0.5472	Remote Similarity	NPC248372
0.5472	Remote Similarity	NPC32441
0.5472	Remote Similarity	NPC482121
0.5472	Remote Similarity	NPC482487
0.5472	Remote Similarity	NPC79943
0.5472	Remote Similarity	NPC270964
0.5424	Remote Similarity	NPC109183
0.5417	Remote Similarity	NPC314329
0.5417	Remote Similarity	NPC603208
0.537	Remote Similarity	NPC177354
0.5333	Remote Similarity	NPC175504
0.5306	Remote Similarity	NPC228184
0.5273	Remote Similarity	NPC274784
0.5273	Remote Similarity	NPC300668
0.5273	Remote Similarity	NPC20709
0.5273	Remote Similarity	NPC215885
0.5273	Remote Similarity	NPC110776
0.5273	Remote Similarity	NPC324386
0.5273	Remote Similarity	NPC110038
0.5246	Remote Similarity	NPC470135
0.5185	Remote Similarity	NPC6407
0.5185	Remote Similarity	NPC545184
0.5179	Remote Similarity	NPC321011
0.5179	Remote Similarity	NPC294852
0.5179	Remote Similarity	NPC188679
0.5179	Remote Similarity	NPC606248
0.5172	Remote Similarity	NPC35150
0.5172	Remote Similarity	NPC106328
0.5088	Remote Similarity	NPC2416
0.5088	Remote Similarity	NPC271590

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC603415 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3686
0.1-0.2	5240
0.2-0.3	211
0.3-0.4	7
0.4-0.5	3
0.5-0.6	2
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
0.6735	Remote Similarity	NPD1550	Phase 2
0.5472	Remote Similarity	NPD1552	Clinical (unspecified phase)
0.5417	Remote Similarity	NPD1547	Clinical (unspecified phase)

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