NPASS Compound

Natural Product: NPC284518

Natural Product ID	NPC284518
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	8-Alpha-O-(4-Hydroxy-2-Methylenebutanoyloxy)Melitensin
IUPAC Name	[(3S,3aR,4S,6S,7R,7aR)-6-ethenyl-7-(3-hydroxyprop-1-en-2-yl)-3,6-dimethyl-2-oxo-3,3a,4,5,7,7a-hexahydro-1-benzofuran-4-yl] 4-hydroxy-2-methylidenebutanoate
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL515222
PubChem CID	25113751
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001283] Terpene lactones [CHEMONTID:0001538] Diterpene lactones

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 54 55 0 0 0 0 0 0 0 0999 V2000 3.0551 0.3249 2.3659 O 0 0 0 0 0 0 0 0 0 0 0 0 4.4163 0.3791 2.2009 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8075 0.4881 0.7572 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3389 -0.6601 -0.0111 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2313 -1.5073 -0.5125 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9462 -0.9445 -0.2984 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6029 -1.9508 -0.9761 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9434 -0.1406 0.1456 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5732 -0.3113 -0.0694 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.1929 -0.5436 1.2167 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6415 -0.8965 0.9374 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6856 -2.2734 0.3902 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3146 -0.8962 2.2846 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0868 -1.8251 3.1854 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2548 0.1716 0.0458 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.4646 0.2422 -1.1867 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0899 0.8169 -0.7744 C 0 0 2 0 0 0 0 0 0 0 0 0 0.5223 1.2057 -2.0797 C 0 0 2 0 0 0 0 0 0 0 0 0 1.0161 2.6381 -1.9662 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6620 1.2563 -2.9798 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5799 1.3985 -4.2492 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7938 1.1241 -2.1878 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.7101 0.1553 -0.0226 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4670 -0.8466 0.4042 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4868 1.3328 -0.5409 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2041 1.5946 -1.8537 O 0 0 0 0 0 0 0 0 0 0 0 0 2.8089 0.5416 3.2856 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9203 -0.5340 2.6368 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8408 1.2591 2.7725 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4651 1.4538 0.3123 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9337 0.5307 0.6740 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2704 -1.3121 -0.3311 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9060 -2.3504 -1.0755 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4649 -1.2344 -0.6752 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2657 -1.4102 1.7387 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1339 0.3531 1.8393 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6455 -2.6765 0.1844 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2251 -2.4215 -0.5481 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0955 -3.0392 1.1163 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0069 -0.0955 2.5010 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4008 -2.6311 2.9895 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5890 -1.7855 4.1330 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0031 1.1406 0.6234 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2097 -0.7447 -1.6383 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2325 1.6784 -0.1119 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2969 0.5147 -2.4375 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9498 2.7198 -1.3927 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1736 3.1110 -2.9437 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2109 3.2110 -1.4417 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5422 -0.8203 0.3362 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0319 -1.7221 0.8299 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5790 1.2234 -0.3825 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1924 2.1920 0.1355 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4382 2.5160 -2.0940 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 2 0 6 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 1 6 11 13 1 0 13 14 2 0 11 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 1 0 18 20 1 0 20 21 2 0 20 22 1 0 15 23 1 0 23 24 2 0 23 25 1 0 25 26 1 0 17 9 1 0 22 16 1 0 1 27 1 0 2 28 1 0 2 29 1 0 3 30 1 0 3 31 1 0 5 32 1 0 5 33 1 0 9 34 1 6 10 35 1 0 10 36 1 0 12 37 1 0 12 38 1 0 12 39 1 0 13 40 1 0 14 41 1 0 14 42 1 0 15 43 1 1 16 44 1 6 17 45 1 1 18 46 1 6 19 47 1 0 19 48 1 0 19 49 1 0 24 50 1 0 24 51 1 0 25 52 1 0 25 53 1 0 26 54 1 0 M END

Standard InCHIKey	VKSVJJJVFPRTAL-XFNMEUKGSA-N
Standard InCHI	InChI=1S/C20H28O6/c1-6-20(5)9-14(25-18(23)11(2)7-8-21)15-13(4)19(24)26-17(15)16(20)12(3)10-22/h6,13-17,21-22H,1-3,7-10H2,4-5H3/t13-,14-,15+,16+,17-,20+/m0/s1
SMILES	OCCC(=C)C(=O)O[C@H]1C[C@@](C)(C=C)[C@@H]([C@@H]2[C@@H]1[C@H](C)C(=O)O2)C(=C)CO

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
NPO10212	Centaurea pullata	Species	Asteraceae	Eukaryota	Aerial parts	Chra Mountain in Blida (North Algeria)	2006-APR	PMID[17979247]
NPO10212	Centaurea pullata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18280170]
NPO10212	Centaurea pullata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO10212	Centaurea pullata	Species	Asteraceae	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
MIC	14
MBC	6
MFC	8

Activity Type	# Activity
Organism	28

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
NPT729	Organism	Micrococcus luteus	Micrococcus luteus	MIC	=	0.4	10'-3micromol/ml	PMID[11012036]
NPT729	Organism	Micrococcus luteus	Micrococcus luteus	MBC	=	0.5	10'-3micromol/ml	PMID[17958396]
NPT21	Organism	Aspergillus niger	Aspergillus niger	MIC	=	0.3	10'-3micromol/ml	PMID[17994701]
NPT21	Organism	Aspergillus niger	Aspergillus niger	MFC	=	0.3	10'-3micromol/ml	PMID[22834923]
NPT4945	Organism	Fusarium tricinctum	Fusarium tricinctum	MIC	=	0.1	10'-3micromol/ml	PMID[18829331]
NPT4945	Organism	Fusarium tricinctum	Fusarium tricinctum	MFC	=	0.2	10'-3micromol/ml	DOI[10.6019/CHEMBL1201861]
NPT3695	Organism	Penicillium funiculosum	Penicillium funiculosum	MIC	=	0.2	10'-3micromol/ml	PMID[17876000]
NPT3695	Organism	Penicillium funiculosum	Penicillium funiculosum	MFC	=	0.3	10'-3micromol/ml	PMID[17876000]
NPT6344	Organism	Penicillium ochrochloron	Penicillium ochrochloron	MIC	=	0.2	10'-3micromol/ml	PMID[17876000]
NPT6344	Organism	Penicillium ochrochloron	Penicillium ochrochloron	MFC	=	0.2	10'-3micromol/ml	PMID[17923492]
NPT79	Organism	Bacillus subtilis	Bacillus subtilis	MIC	=	0.2	10'-3micromol/ml	PMID[22316191]
NPT79	Organism	Bacillus subtilis	Bacillus subtilis	MBC	=	0.4	10'-3micromol/ml	PMID[25517209]
NPT3729	Organism	Pseudomonas tolaasii	Pseudomonas tolaasii	MIC	=	0.5	10'-3micromol/ml	PMID[17958396]
NPT3729	Organism	Pseudomonas tolaasii	Pseudomonas tolaasii	MBC	=	0.8	10'-3micromol/ml	PMID[17958396]
NPT962	Organism	Alternaria alternata	Alternaria alternata	MIC	=	0.1	10'-3micromol/ml	PMID[17067146]
NPT962	Organism	Alternaria alternata	Alternaria alternata	MFC	=	0.1	10'-3micromol/ml	PMID[16989524]
NPT3176	Organism	Aspergillus ochraceus	Aspergillus ochraceus	MIC	=	0.2	10'-3micromol/ml	PMID[17067146]
NPT3176	Organism	Aspergillus ochraceus	Aspergillus ochraceus	MFC	=	0.2	10'-3micromol/ml	PMID[18829331]
NPT17	Organism	Staphylococcus epidermidis	Staphylococcus epidermidis	MIC	=	0.5	10'-3micromol/ml	PMID[11012036]
NPT17	Organism	Staphylococcus epidermidis	Staphylococcus epidermidis	MBC	=	0.8	10'-3micromol/ml	PMID[24144849]
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	=	0.4	10'-3micromol/ml	PMID[17958396]
NPT19	Organism	Escherichia coli	Escherichia coli	MBC	=	0.5	10'-3micromol/ml	PMID[19128055]
NPT185	Organism	Aspergillus flavus	Aspergillus flavus	MIC	=	0.1	10'-3micromol/ml	PMID[26063305]
NPT185	Organism	Aspergillus flavus	Aspergillus flavus	MFC	=	0.2	10'-3micromol/ml	PMID[18829331]
NPT2567	Organism	Trichoderma viride	Hypocrea rufa	MIC	=	0.2	10'-3micromol/ml	Open TG-GATES in vivo data: Biochemistry
NPT2567	Organism	Trichoderma viride	Hypocrea rufa	MFC	=	0.2	10'-3micromol/ml	Open TG-GATES in vivo data: Biochemistry
NPT3608	Organism	Salmonella enteritidis	Salmonella enterica subsp. enterica serovar Enteritidis	MIC	=	0.2	10'-3micromol/ml	PMID[24144848]
NPT3608	Organism	Salmonella enteritidis	Salmonella enterica subsp. enterica serovar Enteritidis	MBC	=	0.4	10'-3micromol/ml	PubChem BioAssay data set

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 NPC284518 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	13910
0.1-0.2	32640
0.2-0.3	3217
0.3-0.4	81
0.4-0.5	5
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	Natural Product ID
0.5645	Remote Similarity	NPC476807
0.5645	Remote Similarity	NPC476806
0.5424	Remote Similarity	NPC308824
0.537	Remote Similarity	NPC153853

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC284518 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5989
0.1-0.2	3133
0.2-0.3	28
0.3-0.4	0
0.4-0.5	0
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