NPASS Compound

Natural Product: NPC326703

Natural Product ID	NPC326703
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	RJLJOXJZWMGEFD-UHFFFAOYSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	6420258
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0003909] Fatty Acyls [CHEMONTID:0000324] Fatty acid esters

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 24 23 0 0 0 0 0 0 0 0999 V2000 3.9498 -0.6888 -0.1332 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3174 0.2972 -1.0935 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0989 0.7658 -0.5480 O 0 0 0 0 0 0 0 0 0 0 0 0 1.0710 -0.1202 -0.2576 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2880 -1.3343 -0.5046 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1885 0.4057 0.3118 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1197 -0.7681 0.5256 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4398 -0.3444 1.1057 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1008 0.6116 0.1754 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2895 0.3102 -0.3365 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5183 -0.5813 0.8978 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0489 -0.5386 -0.1146 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7620 -1.7396 -0.4268 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1579 -0.1770 -2.0791 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9949 1.1816 -1.1582 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0373 0.9957 1.2381 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6675 1.0572 -0.4681 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2925 -1.2182 -0.4855 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5911 -1.5026 1.1305 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2559 0.1770 2.0688 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0507 -1.2188 1.3154 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6112 1.5279 -0.0688 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7986 -0.6273 -0.0914 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7642 0.9944 -1.0034 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 1 0 7 8 1 0 8 9 1 0 9 10 2 0 1 11 1 0 1 12 1 0 1 13 1 0 2 14 1 0 2 15 1 0 6 16 1 0 6 17 1 0 7 18 1 0 7 19 1 0 8 20 1 0 8 21 1 0 9 22 1 0 10 23 1 0 10 24 1 0 M END

Standard InCHIKey	RJLJOXJZWMGEFD-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C8H14O2/c1-3-5-6-7-8(9)10-4-2/h3H,1,4-7H2,2H3
SMILES	CCOC(=O)CCCC=C

Calculated Properties

Physi-Chem Properties

Molecular Weight:	142.1	Volume:	159.232 ? Van der Waals volume.
Dense:	0.892	LogP:	2.159 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	1.99 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-1.835 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	6.0	Rigid Bonds:	2.0
TPSA:	26.3 ? Topological Polar Surface Area.	H-Bond Acceptor:	2.0
H-Bond Donor:	0.0	Rings:	0.0
Heavy Atoms:	2.0

MedChem Properties

QED Drug-Likeness Score:	0.333	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	1.977	Fsp³:	0.625
MCE-18:	0.0 ? 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:	0.006	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.003 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.002 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	1.0	Promiscuous compounds:	0.027

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.607	MDCK Permeability:	-4.738
Pgp-inhibitor:	0.633	Pgp-substrate:	0.01
PAMPA:	0.058 ? 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):	0.029
20% Bioavailability (F20%):	0.764	30% Bioavailability (F30%):	0.889
50% Bioavailability (F50%):	0.932

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.082	MRP1:	0.864
Plasma Protein Binding (PPB):	74.572%	Volume Distribution (VD):	-0.414
Fu:	27.582% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.644
OATP1B3 inhibitor:	0.938	BCRP inhibitor:	0.431
BSEP inhibitor:	0.981

ADMET: Metabolism

CYP1A2-inhibitor:	0.057	CYP1A2-substrate:	0.999
CYP2C19-inhibitor:	0.81	CYP2C19-substrate:	0.586
CYP2C9-inhibitor:	0.044	CYP2C9-substrate:	0.015
CYP2D6-inhibitor:	0.002	CYP2D6-substrate:	0.859
CYP3A4-inhibitor:	0.069	CYP3A4-substrate:	0.984
CYP2B6-substrate:	0.875	CYP2C8-inhibitor:	1.0
HLM stability:	0.998 ? 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):

7.994

Half-life (T1/2):

0.448

ADMET: Toxicity

hERG Blockers:	0.053	hERG Blockers (10um):	0.492
Human Hepatotoxicity (H-HT):	0.144	Drug-induced Liver Injury (DILI):	0.086
AMES Toxicity:	0.277	Rat Oral Acute Toxicity:	0.174
Maximum Recommended Daily Dose:	0.137	Skin Sensitization:	0.854
Carcinogencity:	0.59	Eye Corrosion:	0.987
Eye Irritation:	0.997	Respiratory Toxicity:	0.365
Drug-induced Neurotoxicity:	0.265	Ototoxicity:	0.151
Hematotoxicity:	0.153	Drug-induced Nephrotoxicity:	0.102
Genotoxicity:	0.029	RPMI-8226 Immunitoxicity:	0.029
A549 Cytotoxicity:	0.009	Hek293 Cytotoxicity:	0.023
BCF:	0.83 ? 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:	2.656 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	3.905 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.663 ? 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
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	Nigeria(latitude 80Ã‚Â°N and longitude 4Ã‚Â°E)	2005; 2006	DOI[10.1002/ejlt.201000080]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1007/s11240-015-0761-z]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1007/s11306-010-0259-y]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1007/s11306-014-0638-x]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1007/s11746-997-0093-1]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1007/s12010-013-0354-4]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/j.jarmap.2018.11.004]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/j.phytol.2008.07.007]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	Seeds	Plovdiv, Plovdiv region in South Bulgaria		DOI[10.1051/CTV/20163101031]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1055/S-2006-958077]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1186/s40064-015-0831-z]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1501/Tarimbil_0000001065]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11170689]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	leaf	n.a.	PMID[11312782]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	fruit	n.a.	PMID[11312782]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11408943]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	fruit	n.a.	PMID[12105962]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	Esuela Tecnica Superior de Ingenieros AgrÃƒÂ³nomos de Albacete	2007	PMID[19256538]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20826702]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22537213]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23759170]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	Stalks	n.a.	n.a.	PMID[24521157]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	Seeds	Benedictine Pannonhalma Archabbey, Hungary		PMID[29803478]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31433178]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[37446586]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[37570937]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	Plant	n.a.	n.a.	Database[FooDB]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	Fruits	n.a.		Database[FooDB]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	Stem	n.a.	n.a.	Database[FooDB]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	Leaf Essent. Oil	n.a.	n.a.	Database[FooDB]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[MetaboLights]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO17024	Vitis vinifera	Species	Vitaceae	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 NPC326703 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	23192
0.1-0.2	24831
0.2-0.3	1610
0.3-0.4	167
0.4-0.5	42
0.5-0.6	8
0.6-0.7	8
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
0.6667	Remote Similarity	NPC53541
0.6154	Remote Similarity	NPC250028
0.6154	Remote Similarity	NPC236579
0.6154	Remote Similarity	NPC80234
0.6154	Remote Similarity	NPC203531
0.6154	Remote Similarity	NPC256163
0.6154	Remote Similarity	NPC40597
0.6	Remote Similarity	NPC128061
0.5833	Remote Similarity	NPC143211
0.5517	Remote Similarity	NPC600941
0.5455	Remote Similarity	NPC10316
0.5455	Remote Similarity	NPC200845
0.5455	Remote Similarity	NPC28779
0.5357	Remote Similarity	NPC216130
0.5333	Remote Similarity	NPC310746
0.5217	Remote Similarity	NPC32280

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC326703 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6689
0.1-0.2	2318
0.2-0.3	123
0.3-0.4	15
0.4-0.5	2
0.5-0.6	2
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	Drug ID	Developmental Stage
0.6333	Remote Similarity	NPD5343	Phase 4
0.5938	Remote Similarity	NPD6096	Phase 4
0.5161	Remote Similarity	NPD6097	Approved

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