NPASS Compound

Natural Product: NPC165441

Natural Product ID	NPC165441
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	LGJLRIJXTPDFNB-DVOFNPEISA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	21595545
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000211] Indoles and derivatives [CHEMONTID:0001213] Pyridoindoles [CHEMONTID:0001914] Beta carbolines

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 49 0 0 0 0 0 0 0 0999 V2000 -2.2558 -3.1964 -0.0919 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5454 -1.7656 0.2758 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9186 -0.7712 -0.3658 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9636 -1.1411 -1.4143 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5701 -0.0059 -2.2252 N 0 0 0 0 0 0 0 0 0 0 0 0 0.6082 -0.2976 -3.0183 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6767 -0.8735 -2.1492 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7763 -0.0827 -0.8923 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7373 -0.1542 0.0915 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8735 -0.9544 0.2259 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6798 -0.8244 1.3244 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3295 0.1118 2.2739 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2074 0.8980 2.1352 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3783 0.7828 1.0322 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2534 1.3845 0.6254 N 0 0 0 0 0 0 0 0 0 0 0 0 0.8603 0.8812 -0.5423 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2600 1.1538 -1.4237 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.5285 1.6268 -0.7588 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2542 0.6250 0.0497 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.1024 0.8224 1.5154 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4475 2.2218 1.9423 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7637 2.5292 1.5916 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9533 -3.8449 0.4587 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4358 -3.3801 -1.1710 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2313 -3.4919 0.2002 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2603 -1.5377 1.0583 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4528 -1.8648 -2.1195 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1230 -1.6638 -0.9436 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3996 -0.8955 -3.9078 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9834 0.6966 -3.3858 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6047 -1.9638 -1.9741 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6524 -0.7344 -2.7007 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1378 -1.6951 -0.5398 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5673 -1.4342 1.4513 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9690 0.2215 3.1544 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9251 1.6362 2.8770 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7777 2.1349 1.1660 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0011 1.9571 -2.1602 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3998 2.6257 -0.2953 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2130 1.8605 -1.6463 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3716 0.6963 -0.1486 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7642 0.1400 2.1026 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0827 0.6182 1.9063 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7435 2.9848 1.5789 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4565 2.2493 3.0857 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3010 1.7148 1.7518 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 0 3 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 2 0 10 11 1 0 11 12 2 0 12 13 1 0 13 14 2 0 14 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 1 0 20 21 1 0 21 22 1 0 19 3 1 0 17 5 1 0 16 8 2 0 14 9 1 0 1 23 1 0 1 24 1 0 1 25 1 0 2 26 1 0 4 27 1 0 4 28 1 0 6 29 1 0 6 30 1 0 7 31 1 0 7 32 1 0 10 33 1 0 11 34 1 0 12 35 1 0 13 36 1 0 15 37 1 0 17 38 1 6 18 39 1 0 18 40 1 0 19 41 1 1 20 42 1 0 20 43 1 0 21 44 1 0 21 45 1 0 22 46 1 0 M END

Standard InCHIKey	LGJLRIJXTPDFNB-DVOFNPEISA-N
Standard InCHI	InChI=1S/C19H24N2O/c1-2-13-12-21-9-7-16-15-5-3-4-6-17(15)20-19(16)18(21)11-14(13)8-10-22/h2-6,14,18,20,22H,7-12H2,1H3/b13-2+/t14-,18-/m0/s1
SMILES	C/C=C/1CN2CCc3c4ccccc4[nH]c3[C@@H]2C[C@@H]1CCO

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
NPO15819	Hunteria zeylanica	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19388660]
NPO15819	Hunteria zeylanica	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21524573]
NPO15819	Hunteria zeylanica	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28362501]
NPO15819	Hunteria zeylanica	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO15819	Hunteria zeylanica	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15819	Hunteria zeylanica	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15819	Hunteria zeylanica	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

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 NPC165441 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	29610
0.1-0.2	19195
0.2-0.3	824
0.3-0.4	153
0.4-0.5	30
0.5-0.6	35
0.6-0.7	6
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	Natural Product ID
0.7536	Intermediate Similarity	NPC284645
0.7424	Intermediate Similarity	NPC21174
0.7101	Intermediate Similarity	NPC474897
0.7027	Intermediate Similarity	NPC175474
0.7027	Intermediate Similarity	NPC99921
0.6812	Remote Similarity	NPC185200
0.6364	Remote Similarity	NPC107782
0.6364	Remote Similarity	NPC486454
0.6027	Remote Similarity	NPC472123
0.6027	Remote Similarity	NPC611194
0.6027	Remote Similarity	NPC611315
0.5698	Remote Similarity	NPC280852
0.5696	Remote Similarity	NPC486452
0.5696	Remote Similarity	NPC74591
0.5676	Remote Similarity	NPC229173
0.5625	Remote Similarity	NPC486443
0.5625	Remote Similarity	NPC486446
0.5588	Remote Similarity	NPC88097
0.5541	Remote Similarity	NPC271797
0.5432	Remote Similarity	NPC483467
0.5405	Remote Similarity	NPC317430
0.5319	Remote Similarity	NPC476041
0.5319	Remote Similarity	NPC304926
0.5301	Remote Similarity	NPC52557
0.5301	Remote Similarity	NPC217463
0.5244	Remote Similarity	NPC486449
0.5244	Remote Similarity	NPC63199
0.5244	Remote Similarity	NPC313985
0.5244	Remote Similarity	NPC249150
0.5244	Remote Similarity	NPC111602
0.5244	Remote Similarity	NPC102338
0.5244	Remote Similarity	NPC196251
0.5244	Remote Similarity	NPC273374
0.5244	Remote Similarity	NPC33619
0.5185	Remote Similarity	NPC220151
0.5185	Remote Similarity	NPC19692
0.5181	Remote Similarity	NPC81654
0.5181	Remote Similarity	NPC50503
0.5181	Remote Similarity	NPC607669
0.5063	Remote Similarity	NPC482948
0.5059	Remote Similarity	NPC312870
0.5059	Remote Similarity	NPC199851
0.5059	Remote Similarity	NPC294909
0.5059	Remote Similarity	NPC254240
0.5059	Remote Similarity	NPC128265
0.5059	Remote Similarity	NPC604675

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC165441 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5237
0.1-0.2	3784
0.2-0.3	117
0.3-0.4	7
0.4-0.5	1
0.5-0.6	4
0.6-0.7	0
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
0.5244	Remote Similarity	NPD4601	Phase 4
0.5181	Remote Similarity	NPD4600	Approved
0.5059	Remote Similarity	NPD4500	Approved
0.5059	Remote Similarity	NPD4501	Approved

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