NPASS Compound

Natural Product: NPC612006

Natural Product ID	NPC612006
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	BJOLKYGKSZKIGU-UHFFFAOYSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL1201341
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 38 37 0 0 0 0 0 0 0 0999 V2000 3.9510 -3.1329 -0.6686 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8548 -2.1333 -1.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8967 -1.1486 -0.0183 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7127 0.0339 -0.2692 P 0 0 0 0 0 0 0 0 0 0 0 0 0.8197 -0.3648 -1.4179 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5062 1.4791 -0.6471 O 0 0 0 0 0 0 0 0 0 0 0 0 3.2452 1.9609 0.4061 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9203 3.2424 -0.0597 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5746 0.1888 1.4930 S 0 0 0 0 0 0 0 0 0 0 0 0 -1.1508 0.5952 1.1419 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8590 -0.5095 0.4102 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2270 -0.1279 0.1582 N 0 0 0 0 0 4 0 0 0 0 0 0 -3.3295 0.9821 -0.7621 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9199 0.2593 1.3717 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9671 -1.2358 -0.4235 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0733 -3.2227 0.4426 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9047 -2.8265 -1.1405 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6761 -4.1617 -1.0069 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8558 -2.6024 -0.9790 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0446 -1.6997 -2.0235 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5690 2.2185 1.2316 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0161 1.2485 0.7775 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2231 4.0975 0.1077 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1626 3.2003 -1.1427 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8264 3.3749 0.5605 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6591 0.7031 2.1303 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2687 1.5523 0.6265 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8667 -1.4445 0.9899 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3882 -0.6903 -0.5853 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4264 1.0820 -1.0017 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0162 1.9431 -0.3455 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8399 0.7463 -1.7472 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0078 -0.0416 1.3368 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4377 -0.2979 2.2180 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9230 1.3571 1.5339 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1536 -1.0635 -1.4963 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4352 -2.2068 -0.2623 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9571 -1.3550 0.0611 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 0 4 5 2 0 4 6 1 0 6 7 1 0 7 8 1 0 4 9 1 0 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 12 14 1 0 12 15 1 0 1 16 1 0 1 17 1 0 1 18 1 0 2 19 1 0 2 20 1 0 7 21 1 0 7 22 1 0 8 23 1 0 8 24 1 0 8 25 1 0 10 26 1 0 10 27 1 0 11 28 1 0 11 29 1 0 13 30 1 0 13 31 1 0 13 32 1 0 14 33 1 0 14 34 1 0 14 35 1 0 15 36 1 0 15 37 1 0 15 38 1 0 M CHG 1 12 1 M END

Standard InCHIKey	BJOLKYGKSZKIGU-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C9H23NO3PS/c1-6-12-14(11,13-7-2)15-9-8-10(3,4)5/h6-9H2,1-5H3/q+1
SMILES	CCOP(=O)(OCC)SCC[N+](C)(C)C

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
NPO13391	Streptomyces hygroscopicus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[14563159]
NPO13391	Streptomyces hygroscopicus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[15844961]
NPO13391	Streptomyces hygroscopicus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[16378365]
NPO13391	Streptomyces hygroscopicus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[16453790]
NPO13391	Streptomyces hygroscopicus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[16724461]
NPO13391	Streptomyces hygroscopicus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[17632514]
NPO13391	Streptomyces hygroscopicus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[19231864]
NPO13391	Streptomyces hygroscopicus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[21486005]
NPO13391	Streptomyces hygroscopicus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[21504214]
NPO13391	Streptomyces hygroscopicus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[24224794]
NPO13391	Streptomyces hygroscopicus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[3170341]
NPO13391	Streptomyces hygroscopicus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[3819734]
NPO13391	Streptomyces hygroscopicus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[5549382]
NPO13391	Streptomyces hygroscopicus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[COCONUT]
NPO55802	Streptomyces hygroscopicus SCM-127	Genus	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[COCONUT]
NPO13391	Streptomyces hygroscopicus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[TCMID]
NPO13391	Streptomyces hygroscopicus	Species	Streptomycetaceae	Bacteria	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
AC50	31
HepSE_cirrhosis	1
HepSE_liver function tests abnormal	1
HepSE_jaundice	2
HepSE_bilirubinemia	1
HepSE_cholecystitis	1
HepSE_cholelithiasis	1
HepSE_hepatic failure	1
HepSE_hepatic necrosis	1
HepSE_liver fatty	1
HepSE_hepatomegaly	1
HepSE_Combined Scores	1
HepSE_liver disease	1
HepSE_hepatitis	1
HepSE_elevated liver function tests	1

Activity Type	# Activity
Individual protein	31
Phenotype	15

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT246	Individual protein	Dopamine transporter	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT262	Individual protein	Muscarinic acetylcholine receptor M1	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT244	Individual protein	Dopamine D3 receptor	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT2761	Individual protein	Phosphodiesterase 4A	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT1410	Individual protein	GABA receptor alpha-1 subunit	Rattus norvegicus	AC50	>	30000.0	nM	PMID[37468498]
NPT261	Individual protein	Monoamine oxidase A	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT145	Individual protein	Mu opioid receptor	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT222	Individual protein	Alpha-2a adrenergic receptor	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT1478	Individual protein	Vascular endothelial growth factor receptor 2	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT1788	Individual protein	Alpha-1a adrenergic receptor	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT291	Individual protein	Serotonin 2b (5-HT2b) receptor	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT30	Individual protein	Cyclooxygenase-1	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT153	Individual protein	Androgen Receptor	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT295	Individual protein	Serotonin transporter	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT228	Individual protein	Norepinephrine transporter	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT242	Individual protein	Dopamine D1 receptor	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT108	Individual protein	Estrogen receptor alpha	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT2769	Individual protein	Thromboxane A2 receptor	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT218	Individual protein	Adenosine A3 receptor	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT263	Individual protein	Muscarinic acetylcholine receptor M2	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT204	Individual protein	Acetylcholinesterase	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT987	Individual protein	Histamine H3 receptor	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT98	Individual protein	HERG	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT542	Individual protein	Progesterone receptor	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT92	Individual protein	Serotonin 1a (5-HT1a) receptor	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT5104	Individual protein	Phosphodiesterase 3A	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]
NPT670	Individual protein	Thrombin	Homo sapiens	AC50	>	30000.0	nM	PMID[37468498]

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Unit	Reference
NPT20596	Phenotype	Hepatotoxicity	n.a.	HepSE_cirrhosis	=	n.a.	PMID[22194678]
NPT20596	Phenotype	Hepatotoxicity	n.a.	HepSE_liver function tests abnormal	=	n.a.	PMID[22194678]
NPT20596	Phenotype	Hepatotoxicity	n.a.	HepSE_jaundice	=	n.a.	PMID[22194678]
NPT20596	Phenotype	Hepatotoxicity	n.a.	HepSE_bilirubinemia	=	n.a.	PMID[22194678]
NPT20596	Phenotype	Hepatotoxicity	n.a.	HepSE_cholecystitis	=	n.a.	PMID[22194678]
NPT20596	Phenotype	Hepatotoxicity	n.a.	HepSE_cholelithiasis	=	n.a.	PMID[22194678]
NPT20596	Phenotype	Hepatotoxicity	n.a.	HepSE_hepatic failure	=	n.a.	PMID[22194678]
NPT20596	Phenotype	Hepatotoxicity	n.a.	HepSE_hepatic necrosis	=	n.a.	PMID[22194678]
NPT20596	Phenotype	Hepatotoxicity	n.a.	HepSE_liver fatty	=	n.a.	PMID[22194678]
NPT20596	Phenotype	Hepatotoxicity	n.a.	HepSE_hepatomegaly	=	n.a.	PMID[22194678]
NPT20596	Phenotype	Hepatotoxicity	n.a.	HepSE_Combined Scores	=	n.a.	PMID[22194678]
NPT20596	Phenotype	Hepatotoxicity	n.a.	HepSE_liver disease	=	n.a.	PMID[22194678]

In vivo activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT20596	Phenotype	Hepatotoxicity	n.a.	HepSE_hepatitis	=	0.0	n.a.	PMID[22194678]
NPT20596	Phenotype	Hepatotoxicity	n.a.	HepSE_elevated liver function tests	=	0.0	n.a.	PMID[22194678]

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 NPC612006 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	40682
0.1-0.2	9061
0.2-0.3	85
0.3-0.4	24
0.4-0.5	5
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	Natural Product ID
0.5185	Remote Similarity	NPC1591

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC612006 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7590
0.1-0.2	1478
0.2-0.3	56
0.3-0.4	12
0.4-0.5	9
0.5-0.6	1
0.6-0.7	0
0.7-0.8	0
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	2

Similarity Score	Similarity Level	Drug ID	Developmental Stage
1.0	High Similarity	NPD9681	Phase 4
0.9565	High Similarity	NPD9680	Approved
0.84	Intermediate Similarity	NPD9464	Approved
0.5185	Remote Similarity	NPD9236	Phase 4

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