NPASS Compound

Natural Product: NPC608845

Natural Product ID	NPC608845
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	BAURYGOYSLZFPX-OOCKOLEWSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL563939
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 39 41 0 0 0 0 0 0 0 0999 V2000 -1.5409 3.6518 -0.4920 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7756 2.5686 0.2217 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1072 1.9921 0.5346 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2116 2.5624 0.2929 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8967 0.7289 1.1328 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6188 0.3253 0.5718 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8757 1.6222 0.9066 C 0 0 1 0 0 0 0 0 0 0 0 0 0.5403 1.6001 0.4705 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7107 1.1184 -0.9487 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8195 0.1466 -0.9402 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2103 0.5742 -0.5600 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0437 -0.5338 -0.6387 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5562 -1.1031 -1.2749 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2183 -1.5281 -1.6449 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4776 -2.4628 -0.6886 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6456 -2.0466 0.6999 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.6182 -3.2652 1.6930 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3004 -1.0725 1.1902 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0882 -0.8736 1.2278 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.3824 4.1923 -0.9013 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5462 4.0103 -0.6772 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8218 0.3146 -0.4881 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9398 1.7885 1.9820 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1369 1.0362 1.1966 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9175 2.6459 0.5318 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1714 0.8372 -1.4577 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1113 2.0112 -1.5619 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2117 0.9570 0.4773 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5759 1.3459 -1.2705 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6040 -0.5935 0.1918 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4179 -1.7787 -1.2511 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4895 -0.8114 -2.0528 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4324 -2.1678 -2.6172 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1551 -3.4065 -0.7268 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4350 -2.8296 -1.1757 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8882 -4.1897 1.1560 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4017 -3.0952 2.4473 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3807 -3.3950 2.1082 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4108 -0.8764 2.3353 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 2 3 1 0 3 4 2 0 3 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 1 0 10 13 2 0 13 14 1 0 14 15 1 0 15 16 1 0 16 17 1 1 16 18 1 0 18 19 1 0 7 2 1 0 19 16 1 0 19 6 1 0 1 20 1 0 1 21 1 0 6 22 1 6 7 23 1 1 8 24 1 0 8 25 1 0 9 26 1 0 9 27 1 0 11 28 1 0 11 29 1 0 12 30 1 0 13 31 1 0 14 32 1 0 14 33 1 0 15 34 1 0 15 35 1 0 17 36 1 0 17 37 1 0 17 38 1 0 19 39 1 1 M END

Standard InCHIKey	BAURYGOYSLZFPX-OOCKOLEWSA-N
Standard InCHI	InChI=1S/C15H20O4/c1-9-11-6-5-10(8-16)4-3-7-15(2)13(19-15)12(11)18-14(9)17/h4,11-13,16H,1,3,5-8H2,2H3/b10-4+/t11-,12-,13-,15+/m0/s1
SMILES	C=C1C(=O)O[C@H]2[C@H]1CC/C(CO)=CCC[C@@]1(C)O[C@@H]21

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
NPO20412	Magnolia grandiflora	Species	Magnoliaceae	Eukaryota	Wood	n.a.	n.a.	PMID[7119806]
NPO20412	Magnolia grandiflora	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO20412	Magnolia grandiflora	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20412	Magnolia grandiflora	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20412	Magnolia grandiflora	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO20412	Magnolia grandiflora	Species	Magnoliaceae	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
Activity	5
IC50	18
EC50	4
Ratio IC50	2
Inhibition	1

Activity Type	# Activity
Cell line	21
Unchecked	7
Non-molecular	2

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
NPT393	Cell line	HCT-116	Homo sapiens	Activity	=	2.87	%	PMID[30006167]
NPT461	Cell line	PANC-1	Homo sapiens	IC50	=	10860.0	nM	PMID[30006167]
NPT393	Cell line	HCT-116	Homo sapiens	Activity	=	3.33	%	PMID[30006167]
NPT1535	Cell line	U-87 MG	Homo sapiens	IC50	=	6280.0	nM	PMID[30006167]
NPT65	Cell line	HepG2	Homo sapiens	IC50	=	11970.0	nM	PMID[34847663]
NPT393	Cell line	HCT-116	Homo sapiens	IC50	=	7500.0	nM	PMID[34847663]
NPT660	Cell line	SW480	Homo sapiens	IC50	=	5870.0	nM	PMID[34847663]
NPT393	Cell line	HCT-116	Homo sapiens	Activity	=	12.8	%	PMID[30006167]
NPT181	Cell line	Bel-7402	Homo sapiens	IC50	=	10500.0	nM	PMID[30006167]
NPT139	Cell line	HT-29	Homo sapiens	IC50	=	6950.0	nM	PMID[34847663]
NPT886	Cell line	NIH3T3	Mus musculus	IC50	=	12000.0	nM	PMID[30006167]
NPT81	Cell line	A549	Homo sapiens	IC50	=	9940.0	nM	PMID[30006167]
NPT393	Cell line	HCT-116	Homo sapiens	Activity	=	80.9	%	PMID[30006167]
NPT82	Cell line	MDA-MB-231	Homo sapiens	IC50	=	5590.0	nM	PMID[30739826]
NPT82	Cell line	MDA-MB-231	Homo sapiens	IC50	=	6010.0	nM	PMID[34847663]
NPT393	Cell line	HCT-116	Homo sapiens	IC50	=	4930.0	nM	PMID[30006167]
NPT1045	Cell line	U2OS	Homo sapiens	IC50	=	10700.0	nM	PMID[34847663]
NPT116	Cell line	HL-60	Homo sapiens	IC50	=	10300.0	nM	PMID[28068601]
NPT81	Cell line	A549	Homo sapiens	IC50	=	7490.0	nM	PMID[34847663]
NPT28438	Unchecked	Unchecked	n.a.	EC50	>	10000.0	nM	PMID[30121494]
NPT28438	Unchecked	Unchecked	n.a.	Ratio IC50	=	2.1	n.a.	PMID[30006167]
NPT28438	Unchecked	Unchecked	n.a.	Ratio IC50	=	0.57	n.a.	PMID[30006167]
NPT28438	Unchecked	Unchecked	n.a.	IC50	=	23170.0	nM	PMID[30006167]
NPT28438	Unchecked	Unchecked	n.a.	EC50	=	14000.0	nM	PMID[30121494]
NPT28438	Unchecked	Unchecked	n.a.	EC50	=	24000.0	nM	PMID[30121494]
NPT28438	Unchecked	Unchecked	n.a.	Inhibition	n.a.	n.a.	%	PMID[28525840]
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	EC50	=	15500.0	nM	PMID[28049618]
NPT23712	Cell line	KG-1a	Homo sapiens	IC50	=	6800.0	nM	PMID[28068601]
NPT23713	Cell line	FHC	Homo sapiens	IC50	=	2810.0	nM	PMID[30006167]
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	Activity	=	0.0	%	PMID[19505822]

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
Mus musculus	n.a.	T1/2	=	1.03	hr	PMID[28049618]
Mus musculus	n.a.	CL	=	0.07	L/min	PMID[28049618]
Mus musculus	n.a.	Cmax	=	4500.0	nM	PMID[28049618]
Mus musculus	n.a.	AUC	=	868.3	umol/l.min	PMID[28049618]
Mus musculus	n.a.	F	=	6.7	%	PMID[28049618]
Mus musculus	n.a.	Tmax	=	2.0	hr	PMID[28049618]
Mus musculus	Blood	Drug uptake	n.a.	n.a.	n.a.	PMID[28049618]

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 NPC608845 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	16918
0.1-0.2	27795
0.2-0.3	4644
0.3-0.4	414
0.4-0.5	63
0.5-0.6	10
0.6-0.7	7
0.7-0.8	1
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
0.7708	Intermediate Similarity	NPC38468
0.7708	Intermediate Similarity	NPC192678
0.7708	Intermediate Similarity	NPC319795
0.7708	Intermediate Similarity	NPC50362
0.7708	Intermediate Similarity	NPC488056
0.7708	Intermediate Similarity	NPC605079
0.6604	Remote Similarity	NPC303942
0.6604	Remote Similarity	NPC57405
0.6538	Remote Similarity	NPC49342
0.6538	Remote Similarity	NPC251385
0.625	Remote Similarity	NPC481908
0.625	Remote Similarity	NPC481993
0.6034	Remote Similarity	NPC475659
0.5932	Remote Similarity	NPC487572
0.5932	Remote Similarity	NPC473859
0.569	Remote Similarity	NPC471147
0.5484	Remote Similarity	NPC288876
0.5439	Remote Similarity	NPC70251
0.5439	Remote Similarity	NPC475881
0.5263	Remote Similarity	NPC151770
0.5263	Remote Similarity	NPC7563
0.5167	Remote Similarity	NPC605339
0.5091	Remote Similarity	NPC207188

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC608845 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6550
0.1-0.2	2526
0.2-0.3	71
0.3-0.4	2
0.4-0.5	0
0.5-0.6	0
0.6-0.7	0
0.7-0.8	1
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
0.7708	Intermediate Similarity	NPD1733	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