NPASS Compound

Natural Product: NPC49659

Natural Product ID	NPC49659
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	BEZRAMBFCSSHHE-QUBQUEJXSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	11514622
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0003909] Fatty Acyls [CHEMONTID:0001334] Fatty alcohols [CHEMONTID:0002951] Long-chain fatty alcohols

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 44 43 0 0 0 0 0 0 0 0999 V2000 7.1436 -2.4052 1.5164 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1136 -1.6422 1.1946 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2333 -0.2361 0.7722 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6762 -0.0104 -0.6248 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2124 -0.3734 -0.6965 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4524 0.4957 0.2817 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9527 0.1674 0.2529 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3221 1.0574 1.2222 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3971 1.9411 0.9687 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1116 2.1196 -0.3922 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.4192 1.4180 -0.4563 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4896 0.8661 -0.5155 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7356 0.1964 -0.5803 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8218 -0.3641 -0.6400 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1291 -1.0154 -0.7263 C 0 0 2 0 0 0 0 0 0 0 0 0 -7.1924 -0.1361 -0.0941 C 0 0 2 0 0 0 0 0 0 0 0 0 -8.5566 -0.7938 -0.2867 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.2385 1.0925 -0.7340 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0385 -2.2468 -0.1311 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3334 3.5145 -0.5413 O 0 0 0 0 0 0 0 0 0 0 0 0 8.1419 -2.0058 1.4779 H 0 0 0 0 0 0 0 0 0 0 0 0 7.0087 -3.4242 1.8189 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1199 -2.0676 1.2409 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8188 0.4373 1.5227 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3390 -0.0108 0.7058 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8926 0.9896 -0.9995 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2188 -0.7314 -1.2887 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8704 -0.1766 -1.7218 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0990 -1.4267 -0.4316 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7911 0.3365 1.3123 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5398 1.5689 0.0410 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8589 -0.9231 0.5392 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6342 0.2251 -0.7779 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6569 0.9794 2.2717 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0075 2.5623 1.7876 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5544 1.8615 -1.2099 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4465 -1.1755 -1.7817 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0411 0.0125 0.9906 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.6386 -1.0813 -1.3615 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.6810 -1.6636 0.3921 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.3288 -0.0369 -0.1027 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.1616 1.3552 -0.9492 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2595 -3.0014 -0.7552 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4170 3.7510 -1.4937 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 2 3 1 0 3 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 2 0 9 10 1 0 10 11 1 0 11 12 3 0 12 13 1 0 13 14 3 0 14 15 1 0 15 16 1 0 16 17 1 0 16 18 1 0 15 19 1 0 10 20 1 0 1 21 1 0 1 22 1 0 2 23 1 0 3 24 1 0 3 25 1 0 4 26 1 0 4 27 1 0 5 28 1 0 5 29 1 0 6 30 1 0 6 31 1 0 7 32 1 0 7 33 1 0 8 34 1 0 9 35 1 0 10 36 1 6 15 37 1 6 16 38 1 1 17 39 1 0 17 40 1 0 17 41 1 0 18 42 1 0 19 43 1 0 20 44 1 0 M END

Standard InCHIKey	BEZRAMBFCSSHHE-QUBQUEJXSA-N
Standard InCHI	InChI=1S/C17H24O3/c1-3-4-5-6-7-8-9-12-16(19)13-10-11-14-17(20)15(2)18/h3,9,12,15-20H,1,4-8H2,2H3/b12-9-/t15-,16-,17+/m0/s1
SMILES	C=CCCCCC/C=C[C@@H](C#CC#C[C@H]([C@H](C)O)O)O

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
NPO7728	Vitex agnus-castus	Species	Lamiaceae	Eukaryota	n.a.	fruit	n.a.	PMID[17262892]
NPO7728	Vitex agnus-castus	Species	Lamiaceae	Eukaryota	n.a.	fruit	n.a.	PMID[21163339]
NPO7728	Vitex agnus-castus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[37446759]
NPO14730	Bonnetia dinizii	Species	Bonnetiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO7728	Vitex agnus-castus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO2090	Baccharis thesioides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO5406	Veronica chamaedrys	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9385	Glycosmis ovoidea	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14084	Roccella fucoides	Species	Roccellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2509	Strombus gigas	Species	Strombidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14730	Bonnetia dinizii	Species	Bonnetiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7728	Vitex agnus-castus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2090	Baccharis thesioides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO368	Dendroaspis angusticeps	Species	Elapidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18458	Raukaua simplex	Species	Araliaceae	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

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

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 NPC49659 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	31492
0.1-0.2	17530
0.2-0.3	665
0.3-0.4	91
0.4-0.5	39
0.5-0.6	17
0.6-0.7	4
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC93639
0.7812	Intermediate Similarity	NPC124183
0.7812	Intermediate Similarity	NPC482802
0.7647	Intermediate Similarity	NPC153538
0.7222	Intermediate Similarity	NPC482801
0.7059	Intermediate Similarity	NPC91226
0.7059	Intermediate Similarity	NPC243546
0.7059	Intermediate Similarity	NPC31194
0.7059	Intermediate Similarity	NPC248884
0.7027	Intermediate Similarity	NPC142092
0.697	Remote Similarity	NPC243813
0.641	Remote Similarity	NPC35141
0.6389	Remote Similarity	NPC72699
0.6047	Remote Similarity	NPC212730
0.5897	Remote Similarity	NPC484320
0.5897	Remote Similarity	NPC168510
0.5778	Remote Similarity	NPC265551
0.561	Remote Similarity	NPC85079
0.561	Remote Similarity	NPC151782
0.5581	Remote Similarity	NPC66460
0.5581	Remote Similarity	NPC325929
0.5581	Remote Similarity	NPC271282
0.5385	Remote Similarity	NPC321763
0.5385	Remote Similarity	NPC101616
0.5152	Remote Similarity	NPC125122
0.5152	Remote Similarity	NPC471276
0.5152	Remote Similarity	NPC471280
0.5152	Remote Similarity	NPC471281
0.5143	Remote Similarity	NPC249670
0.5128	Remote Similarity	NPC481854
0.5111	Remote Similarity	NPC29697

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC49659 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	8023
0.1-0.2	1099
0.2-0.3	26
0.3-0.4	2
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