NPASS Compound

Natural Product: NPC305182

Natural Product ID	NPC305182
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Gama-Nonalactone
IUPAC Name	3-pentyloxolan-2-one
Synonyms	Gama-Nonalactone
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL476333
PubChem CID	559675
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000050] Lactones [CHEMONTID:0001245] Gamma butyrolactones

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 27 27 0 0 0 0 0 0 0 0999 V2000 4.1028 -0.3160 -0.3662 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7065 -0.2812 0.2075 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8135 0.6796 -0.5311 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4331 0.7457 -0.0013 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3233 -0.5414 -0.0310 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6975 -0.2652 0.5473 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4401 0.7761 -0.2524 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8708 0.3153 -0.1689 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8667 -0.9645 0.4204 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5708 -1.4650 0.5128 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1849 -2.6615 0.5593 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5230 -1.3216 -0.1324 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7679 0.4126 0.1565 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1130 -0.1768 -1.4618 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2877 -1.2844 0.1593 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8068 0.0721 1.2685 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2724 1.6867 -0.4311 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8771 0.4215 -1.6062 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4509 1.1124 1.0354 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1362 1.4859 -0.6015 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4179 -0.9815 -1.0411 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1404 -1.3106 0.6479 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5446 0.0818 1.5988 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1271 0.7768 -1.3323 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2818 1.8031 0.1127 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4907 1.0023 0.4488 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3427 0.1978 -1.1778 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 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 2 0 10 6 1 0 1 12 1 0 1 13 1 0 1 14 1 0 2 15 1 0 2 16 1 0 3 17 1 0 3 18 1 0 4 19 1 0 4 20 1 0 5 21 1 0 5 22 1 0 6 23 1 0 7 24 1 0 7 25 1 0 8 26 1 0 8 27 1 0 M END

Standard InCHIKey	ZWYZHNNHSZXTTG-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C9H16O2/c1-2-3-4-5-8-6-7-11-9(8)10/h8H,2-7H2,1H3
SMILES	CCCCCC1CCOC1=O

Calculated Properties

Physi-Chem Properties

Molecular Weight:	156.12	Volume:	170.608 ? Van der Waals volume.
Dense:	0.915	LogP:	2.189 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	2.038 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-2.126 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	4.0	Rigid Bonds:	6.0
TPSA:	26.3 ? Topological Polar Surface Area.	H-Bond Acceptor:	2.0
H-Bond Donor:	0.0	Rings:	1.0
Heavy Atoms:	2.0

MedChem Properties

QED Drug-Likeness Score:	0.46	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	2.756	Fsp³:	0.889
MCE-18:	11.765 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Rejected	GSK Rule:	Rejected
Golden Triangle Rule:	Accepted	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.009	Fluc inhibitor:	0.002 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.006 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.016 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.999	Promiscuous compounds:	0.198

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.913	MDCK Permeability:	-4.662
Pgp-inhibitor:	0.066	Pgp-substrate:	0.048
PAMPA:	0.17 ? The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).	Human Intestinal Absorption (HIA):	0.038
20% Bioavailability (F20%):	0.068	30% Bioavailability (F30%):	0.045
50% Bioavailability (F50%):	0.05

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.202	MRP1:	0.632
Plasma Protein Binding (PPB):	91.419%	Volume Distribution (VD):	0.194
Fu:	9.349% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.727
OATP1B3 inhibitor:	0.974	BCRP inhibitor:	0.015
BSEP inhibitor:	0.437

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.967
CYP2C19-inhibitor:	0.943	CYP2C19-substrate:	0.374
CYP2C9-inhibitor:	0.57	CYP2C9-substrate:	0.018
CYP2D6-inhibitor:	0.013	CYP2D6-substrate:	0.572
CYP3A4-inhibitor:	0.022	CYP3A4-substrate:	0.998
CYP2B6-substrate:	0.959	CYP2C8-inhibitor:	0.945
HLM stability:	0.803 ? Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):

6.487

Half-life (T1/2):

0.972

ADMET: Toxicity

hERG Blockers:	0.134	hERG Blockers (10um):	0.556
Human Hepatotoxicity (H-HT):	0.427	Drug-induced Liver Injury (DILI):	0.487
AMES Toxicity:	0.182	Rat Oral Acute Toxicity:	0.178
Maximum Recommended Daily Dose:	0.136	Skin Sensitization:	0.861
Carcinogencity:	0.559	Eye Corrosion:	0.984
Eye Irritation:	0.996	Respiratory Toxicity:	0.486
Drug-induced Neurotoxicity:	0.46	Ototoxicity:	0.181
Hematotoxicity:	0.278	Drug-induced Nephrotoxicity:	0.284
Genotoxicity:	0.002	RPMI-8226 Immunitoxicity:	0.044
A549 Cytotoxicity:	0.093	Hek293 Cytotoxicity:	0.047
BCF:	1.061 ? Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].	IGC50:	3.504 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.899 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.436 ? 96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/j.jfca.2004.07.004]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/j.jfca.2005.08.001]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12379786]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18460139]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23507362]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	Cotyledon	n.a.	n.a.	Database[FooDB]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	Seed Oil	n.a.	n.a.	Database[FooDB]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO7530	Cucumis sativus	Species	Cucurbitaceae	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	1

Activity Type	# Activity
Individual protein	1

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1652	Individual protein	Serum paraoxonase/arylesterase 1	Homo sapiens	Activity	=	14.47	umol/min/mg	PMID[18572410]

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 NPC305182 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	21719
0.1-0.2	26044
0.2-0.3	1918
0.3-0.4	153
0.4-0.5	20
0.5-0.6	1
0.6-0.7	0
0.7-0.8	0
0.8-0.85	0
0.85-0.9	1
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.875	High Similarity	NPC282440
0.5172	Remote Similarity	NPC601675

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC305182 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5672
0.1-0.2	3232
0.2-0.3	229
0.3-0.4	17
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