NPASS Compound

Natural Product: NPC609069

Natural Product ID	NPC609069
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	BYHVZDRLSCCTND-UHFFFAOYSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL1376695
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 34 36 0 0 0 0 0 0 0 0999 V2000 -6.2285 0.8215 -0.3674 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8729 1.1395 -0.1923 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.9160 0.1679 0.1121 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5932 0.5057 0.2788 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6604 -0.4464 0.5763 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2515 -0.0598 0.7498 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4331 -0.1490 -0.6054 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8635 0.2367 -0.4647 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3109 1.5287 -0.6048 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6484 1.8430 -0.4659 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5421 0.8359 -0.1819 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1401 -0.4873 -0.0305 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7924 -0.7412 -0.1803 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2635 -1.2600 0.2490 O 0 0 0 0 0 0 0 0 0 0 0 0 6.4187 -0.4653 0.1538 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9126 0.8324 0.0115 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.0157 -1.6869 0.7053 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2480 -2.0480 0.5570 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5705 -3.2587 0.6869 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2646 -1.1573 0.2550 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8071 1.7538 -0.1748 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3593 0.4599 -1.4104 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5396 0.0981 0.3969 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3043 1.5641 0.1664 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1634 1.0047 1.0848 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3051 -0.7466 1.4194 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0811 0.4140 -1.3863 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3844 -1.2375 -0.8970 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5870 2.2967 -0.8274 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0132 2.8577 -0.5741 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4842 -1.7722 -0.0617 H 0 0 0 0 0 0 0 0 0 0 0 0 7.0961 -0.7701 -0.6654 H 0 0 0 0 0 0 0 0 0 0 0 0 6.9721 -0.5792 1.1283 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2917 -1.4946 0.1369 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 5 6 1 0 6 7 1 0 7 8 1 0 8 9 2 0 9 10 1 0 10 11 2 0 11 12 1 0 12 13 2 0 12 14 1 0 14 15 1 0 15 16 1 0 5 17 1 0 17 18 1 0 18 19 2 0 18 20 1 0 20 3 2 0 13 8 1 0 16 11 1 0 1 21 1 0 1 22 1 0 1 23 1 0 4 24 1 0 6 25 1 0 6 26 1 0 7 27 1 0 7 28 1 0 9 29 1 0 10 30 1 0 13 31 1 0 15 32 1 0 15 33 1 0 20 34 1 0 M END

Standard InCHIKey	BYHVZDRLSCCTND-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C15H14O5/c1-17-12-7-11(20-15(16)8-12)4-2-10-3-5-13-14(6-10)19-9-18-13/h3,5-8H,2,4,9H2,1H3
SMILES	COc1cc(CCc2ccc3c(c2)OCO3)oc(=O)c1

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
NPO3346	Piper sanctum	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO3346	Piper sanctum	Species	Piperaceae	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
Potency	8
IC50	5
MIC	2

Activity Type	# Activity
Individual protein	5
Cell line	1
Unchecked	1
Organism	8

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT135	Individual protein	Chromobox protein homolog 1	Homo sapiens	Potency	n.a.	89125.1	nM	PubChem BioAssay data set
NPT531	Individual protein	Nuclear receptor ROR-gamma	Mus musculus	Potency	=	22387.2	nM	PubChem BioAssay data set
NPT535	Individual protein	Parathyroid hormone receptor	Homo sapiens	Potency	n.a.	112201.8	nM	PubChem BioAssay data set
NPT5	Individual protein	Histone-lysine N-methyltransferase, H3 lysine-9 specific 3	Homo sapiens	Potency	n.a.	1412.5	nM	PubChem BioAssay data set
NPT64	Individual protein	ATPase family AAA domain-containing protein 5	Homo sapiens	Potency	n.a.	20587.8	nM	PubChem BioAssay data set

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT839	Cell line	L6	Rattus norvegicus	IC50	=	150000.0	nM	PMID[22285027]
NPT28438	Unchecked	Unchecked	n.a.	Potency	=	29092.9	nM	PubChem BioAssay data set
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	>	18000.0	nM	PMID[22285027]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	Potency	n.a.	2078.7	nM	PubChem BioAssay data set
NPT844	Organism	Trypanosoma brucei rhodesiense	Trypanosoma brucei rhodesiense	IC50	>	330000.0	nM	PMID[22285027]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	Potency	n.a.	7375.3	nM	PubChem BioAssay data set
NPT88	Organism	Mycobacterium tuberculosis	Mycobacterium tuberculosis	MIC	=	32.0	ug.mL-1	PMID[23369537]
NPT580	Organism	Trypanosoma cruzi	Trypanosoma cruzi	IC50	>	330000.0	nM	PMID[22285027]
NPT88	Organism	Mycobacterium tuberculosis	Mycobacterium tuberculosis	MIC	>	360000.0	nM	PMID[22285027]
NPT633	Organism	Leishmania donovani	Leishmania donovani	IC50	>	330000.0	nM	PMID[22285027]

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 NPC609069 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	31026
0.1-0.2	16829
0.2-0.3	1800
0.3-0.4	179
0.4-0.5	20
0.5-0.6	3
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	Natural Product ID
0.6275	Remote Similarity	NPC96625
0.5918	Remote Similarity	NPC604144
0.5469	Remote Similarity	NPC204385
0.5161	Remote Similarity	NPC206201

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC609069 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4515
0.1-0.2	4433
0.2-0.3	195
0.3-0.4	6
0.4-0.5	1
0.5-0.6	0
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
		NPD

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