NPASS Compound

Natural Product: NPC600620

Natural Product ID	NPC600620
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	SPCIYGNTAMCTRO-UHFFFAOYSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL65547
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds]

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 31 32 0 0 0 0 0 0 0 0999 V2000 -3.8203 -0.7496 0.4064 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8971 0.1495 -0.1458 N 0 0 0 0 0 0 0 0 0 0 0 0 -3.2794 1.4880 -0.2868 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5841 -0.2533 -0.4176 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7645 -0.5355 0.8224 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6201 -0.9482 0.4915 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1096 -2.2363 0.4527 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4005 -2.1916 0.0889 N 0 0 0 0 0 0 0 0 0 0 0 0 2.7912 -0.9232 -0.1157 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0163 -0.3579 -0.4957 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1633 1.0039 -0.6345 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0588 1.7916 -0.3844 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8478 1.2293 -0.0079 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7314 2.0158 0.2500 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6816 -0.1373 0.1354 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7518 -0.2528 0.7486 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1478 -1.4822 -0.3873 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4112 -1.3026 1.2901 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1073 1.7335 0.3965 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4226 2.1586 0.0132 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5979 1.7453 -1.3316 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0571 0.4704 -1.0395 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6193 -1.2630 -0.9482 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2179 -1.3537 1.4264 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7360 0.3632 1.5006 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4974 -3.1163 0.6944 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0021 -3.0483 -0.0144 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8412 -1.0103 -0.6756 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0947 1.4751 -0.9255 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1592 2.8743 -0.4878 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3989 2.6635 -0.4187 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 2 4 1 0 4 5 1 0 5 6 1 0 6 7 2 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 1 0 13 15 2 0 15 6 1 0 15 9 1 0 1 16 1 0 1 17 1 0 1 18 1 0 3 19 1 0 3 20 1 0 3 21 1 0 4 22 1 0 4 23 1 0 5 24 1 0 5 25 1 0 7 26 1 0 8 27 1 0 10 28 1 0 11 29 1 0 12 30 1 0 14 31 1 0 M END

Standard InCHIKey	SPCIYGNTAMCTRO-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C12H16N2O/c1-14(2)7-6-9-8-13-10-4-3-5-11(15)12(9)10/h3-5,8,13,15H,6-7H2,1-2H3
SMILES	CN(C)CCc1c[nH]c2cccc(O)c12

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
NPO64097	Psilocybe arcana	Species	Strophariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO51592	Psilocybe bohemica	Species	Strophariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO47638	Psilocybe maxicana	Genus	Strophariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO6818	Psilocybe mexicana	Species	Strophariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO5609	Psilocybe semilanceata	Species	Strophariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO5609	Psilocybe semilanceata	Species	Strophariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6818	Psilocybe mexicana	Species	Strophariaceae	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

Activity Type	# Activity
EC50	15
Binding	2
Emax	4
Ki	5
IC50	3
Efficacy	4
Potency	3
K0.5	1
Ratio	1
pKa	3
AC50	6
Poct	1
Max	1

Activity Type	# Activity
Individual protein	36
Organism	2
No target	4
Unchecked	7

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1778	Individual protein	Serotonin 2a (5-HT2a) receptor	Rattus norvegicus	EC50	=	2300.0	nM	PMID[12877591]
NPT290	Individual protein	Serotonin 2a (5-HT2a) receptor	Homo sapiens	EC50	=	75.2	nM	PMID[34676027]
NPT290	Individual protein	Serotonin 2a (5-HT2a) receptor	Homo sapiens	Emax	=	89.0	%	PMID[38505858]
NPT291	Individual protein	Serotonin 2b (5-HT2b) receptor	Homo sapiens	Ki	=	4.6	nM	PMID[38516602]
NPT290	Individual protein	Serotonin 2a (5-HT2a) receptor	Homo sapiens	EC50	=	4.266	nM	PMID[32077284]
NPT1778	Individual protein	Serotonin 2a (5-HT2a) receptor	Rattus norvegicus	Ki	=	323.0	nM	PMID[18296055]
NPT290	Individual protein	Serotonin 2a (5-HT2a) receptor	Homo sapiens	EC50	=	22.0	nM	PMID[38505858]
NPT290	Individual protein	Serotonin 2a (5-HT2a) receptor	Homo sapiens	EC50	=	19.95	nM	PMID[38505858]
NPT290	Individual protein	Serotonin 2a (5-HT2a) receptor	Homo sapiens	EC50	=	4.3	nM	PMID[32077284]
NPT290	Individual protein	Serotonin 2a (5-HT2a) receptor	Homo sapiens	EC50	=	24.0	nM	PMID[16061378]
NPT290	Individual protein	Serotonin 2a (5-HT2a) receptor	Homo sapiens	EC50	=	6.5	nM	PMID[35450349]
NPT290	Individual protein	Serotonin 2a (5-HT2a) receptor	Homo sapiens	EC50	<	1000.0	nM	PMID[35586424]
NPT290	Individual protein	Serotonin 2a (5-HT2a) receptor	Homo sapiens	EC50	=	6.5	nM	PMID[34917241]
NPT290	Individual protein	Serotonin 2a (5-HT2a) receptor	Homo sapiens	Ki	=	107.2	nM	PMID[38516602]
NPT292	Individual protein	Serotonin 2c (5-HT2c) receptor	Homo sapiens	IC50	=	7.79	nM	PMID[34917242]
NPT1778	Individual protein	Serotonin 2a (5-HT2a) receptor	Rattus norvegicus	Ki	=	390.0	nM	PMID[10514296]
NPT1778	Individual protein	Serotonin 2a (5-HT2a) receptor	Rattus norvegicus	Efficacy	n.a.	n.a.	n.a.	PMID[18296055]
NPT290	Individual protein	Serotonin 2a (5-HT2a) receptor	Homo sapiens	Efficacy	=	82.0	%	PMID[34917242]
NPT1778	Individual protein	Serotonin 2a (5-HT2a) receptor	Rattus norvegicus	K0.5	=	6.0	nM	PMID[10514296]
NPT290	Individual protein	Serotonin 2a (5-HT2a) receptor	Homo sapiens	Emax	=	73.0	%	PMID[32077284]
NPT2695	Individual protein	Serotonin 2a (5-HT2a) receptor	Mus musculus	Emax	=	72.0	%	PMID[32077284]
NPT291	Individual protein	Serotonin 2b (5-HT2b) receptor	Homo sapiens	Efficacy	=	63.0	%	PMID[34917242]
NPT291	Individual protein	Serotonin 2b (5-HT2b) receptor	Homo sapiens	EC50	=	58.0	nM	PMID[16061378]
NPT2695	Individual protein	Serotonin 2a (5-HT2a) receptor	Mus musculus	EC50	=	9.9	nM	PMID[32077284]
NPT2695	Individual protein	Serotonin 2a (5-HT2a) receptor	Mus musculus	EC50	=	9.772	nM	PMID[32077284]
NPT292	Individual protein	Serotonin 2c (5-HT2c) receptor	Homo sapiens	EC50	=	30.0	nM	PMID[16061378]
NPT290	Individual protein	Serotonin 2a (5-HT2a) receptor	Homo sapiens	IC50	=	8.34	nM	PMID[34917242]
NPT292	Individual protein	Serotonin 2c (5-HT2c) receptor	Homo sapiens	Efficacy	=	95.0	%	PMID[34917242]
NPT290	Individual protein	Serotonin 2a (5-HT2a) receptor	Homo sapiens	EC50	<	1000.0	nM	PMID[36105333]
NPT1778	Individual protein	Serotonin 2a (5-HT2a) receptor	Rattus norvegicus	Ki	=	25.0	nM	PMID[12877591]
NPT290	Individual protein	Serotonin 2a (5-HT2a) receptor	Homo sapiens	Emax	=	95.6	%	PMID[34917241]
NPT291	Individual protein	Serotonin 2b (5-HT2b) receptor	Homo sapiens	IC50	=	1.07	nM	PMID[34917242]
NPT50	Individual protein	Tyrosyl-DNA phosphodiesterase 1	Homo sapiens	Potency	n.a.	21469.6	nM	PubChem BioAssay data set
NPT50	Individual protein	Tyrosyl-DNA phosphodiesterase 1	Homo sapiens	Potency	n.a.	27028.6	nM	PubChem BioAssay data set
NPT92	Individual protein	Serotonin 1a (5-HT1a) receptor	Homo sapiens	Binding	n.a.	n.a.	n.a.	PMID[12877591]
NPT438	Individual protein	Serotonin 2c (5-HT2c) receptor	Rattus norvegicus	Binding	n.a.	n.a.	n.a.	PMID[12877591]

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT28833	No target	No relevant target	n.a.	pKa	=	8.47	n.a.	PMID[6259355]
NPT28438	Unchecked	Unchecked	n.a.	AC50	n.a.	15848.9	nM	PubChem BioAssay data set
NPT28438	Unchecked	Unchecked	n.a.	Ac50	n.a.	35.48	uM	PubChem BioAssay data set
NPT28438	Unchecked	Unchecked	n.a.	Ac50	n.a.	15.85	uM	PubChem BioAssay data set
NPT28438	Unchecked	Unchecked	n.a.	AC50	n.a.	39810.7	nM	PubChem BioAssay data set
NPT28438	Unchecked	Unchecked	n.a.	Potency	n.a.	44668.4	nM	PubChem BioAssay data set
NPT28833	No target	No relevant target	n.a.	pKa	=	3.3	n.a.	PMID[6259355]
NPT28438	Unchecked	Unchecked	n.a.	AC50	n.a.	35481.3	nM	PubChem BioAssay data set
NPT28833	No target	No relevant target	n.a.	pKa	=	42.1	n.a.	PMID[6259355]
NPT28833	No target	No relevant target	n.a.	Poct	=	0.68	n.a.	PMID[6259355]
NPT28438	Unchecked	Unchecked	n.a.	Ac50	n.a.	39.81	uM	PubChem BioAssay data set
NPT605	Organism	Homo sapiens	Homo sapiens	Ratio	=	32.0	n.a.	PMID[592329]

In vivo activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	Max	=	46.0	%	PMID[12877591]

Experimental ADME

Experiment Model	Experiment Tissue	ADME Type	ADME Relation	ADME Value	ADME Unit	Reference
n.a.	n.a.	LogP	=	1.45	n.a.	PMID[6259355]
n.a.	n.a.	LogP	=	0.191	n.a.	PMID[18296055]
Homo sapiens	Liver	CL	<	15.9	mL.min-1.g-1	PMID[35450349]
Homo sapiens	Liver	CL	=	11.81	mL.min-1.g-1	PMID[34676027]
Homo sapiens	Liver	T1/2	>	2.417	hr	PMID[35450349]
Rattus norvegicus	Brain	T1/2	=	1.913	hr	PMID[35450349]
Homo sapiens	Liver	T1/2	=	1.955	hr	PMID[34676027]

Experimental Toxicity

Quantitative toxicity

Experiment Model	Experiment Organism	Toxicity Type	Toxicity Relation	Toxicity Value	Toxicity Unit	Reference
-	Mus musculus	LD50	=	3.017954896	mg/kg	TOXRIC

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 NPC600620 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	36168
0.1-0.2	12925
0.2-0.3	675
0.3-0.4	81
0.4-0.5	4
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	Natural Product ID
0.6	Remote Similarity	NPC171171
0.6	Remote Similarity	NPC602417
0.5833	Remote Similarity	NPC73767
0.5088	Remote Similarity	NPC106937

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC600620 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6387
0.1-0.2	2607
0.2-0.3	128
0.3-0.4	23
0.4-0.5	4
0.5-0.6	1
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
0.5088	Remote Similarity	NPD802	Phase 3

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