NPASS Compound

Natural Product: NPC510963

Natural Product ID	NPC510963
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Heptanoic acid, (3Z)-3-hexenyl ester
IUPAC Name	hex-3-enyl heptanoate
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
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 38 0 0 0 0 0 0 0 0999 V2000 -6.2342 0.5412 0.3847 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5887 -0.3120 -0.7027 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4865 0.4275 -1.3234 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2569 0.0450 -1.3385 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7643 -1.2009 -0.7317 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7166 -0.9006 0.3521 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6566 -0.2035 -0.2738 O 0 0 0 0 0 0 0 0 0 0 0 0 0.4212 0.1852 0.5448 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4023 -0.0947 1.7597 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5717 0.9226 -0.0240 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6465 1.1793 0.9778 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3102 -0.0339 1.5404 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0365 -0.8932 0.5820 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2366 -0.3685 -0.1058 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1007 0.8129 -0.9941 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4914 0.8807 1.1068 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9983 -0.0746 0.8710 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7406 1.4398 -0.0365 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3625 -0.5409 -1.5002 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3618 -1.2658 -0.2465 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7625 1.3829 -1.8080 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5007 0.6834 -1.8385 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2870 -1.8063 -1.5520 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4945 -1.8462 -0.2625 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3910 -1.8217 0.8491 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2462 -0.2872 1.1184 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2005 1.9270 -0.3777 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8821 0.3434 -0.9163 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3831 1.9163 0.6315 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1365 1.6998 1.8632 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0157 0.3177 2.3603 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5443 -0.6324 2.1081 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2455 -1.8696 1.1093 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2963 -1.1525 -0.2511 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6378 -1.2469 -0.7249 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0635 -0.1649 0.6685 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0822 0.9134 -1.3841 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3876 1.7702 -0.4997 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7395 0.6922 -1.9359 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 2 3 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 2 0 8 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 1 16 1 0 1 17 1 0 1 18 1 0 2 19 1 0 2 20 1 0 3 21 1 0 4 22 1 0 5 23 1 0 5 24 1 0 6 25 1 0 6 26 1 0 10 27 1 0 10 28 1 0 11 29 1 0 11 30 1 0 12 31 1 0 12 32 1 0 13 33 1 0 13 34 1 0 14 35 1 0 14 36 1 0 15 37 1 0 15 38 1 0 15 39 1 0 M END

Standard InCHIKey	KBBLMMCEHYHHIW-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C13H24O2/c1-3-5-7-9-11-13(14)15-12-10-8-6-4-2/h6,8H,3-5,7,9-12H2,1-2H3
SMILES	CCC=CCCOC(=O)CCCCCC

Calculated Properties

Physi-Chem Properties

Molecular Weight:	212.18	Volume:	245.712 ? Van der Waals volume.
Dense:	0.864	LogP:	4.423 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.361 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-3.904 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	10.0	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:	0.329	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	2.171	Fsp³:	0.769
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:	Accepted	GSK Rule:	Accepted
Golden Triangle Rule:	Rejected	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.014	Fluc inhibitor:	0.018 ? 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:	0.007 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.999	Promiscuous compounds:	0.302

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-4.87	MDCK Permeability:	-4.648
Pgp-inhibitor:	0.3	Pgp-substrate:	0.139
PAMPA:	0.022 ? 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):	0.074
20% Bioavailability (F20%):	0.395	30% Bioavailability (F30%):	0.324
50% Bioavailability (F50%):	0.461

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.531	MRP1:	0.921
Plasma Protein Binding (PPB):	97.084%	Volume Distribution (VD):	-0.462
Fu:	2.855% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.053
OATP1B3 inhibitor:	0.664	BCRP inhibitor:	0.178
BSEP inhibitor:	0.993

ADMET: Metabolism

CYP1A2-inhibitor:	0.004	CYP1A2-substrate:	1.0
CYP2C19-inhibitor:	0.205	CYP2C19-substrate:	0.991
CYP2C9-inhibitor:	0.71	CYP2C9-substrate:	0.884
CYP2D6-inhibitor:	0.19	CYP2D6-substrate:	0.997
CYP3A4-inhibitor:	0.259	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.009	CYP2C8-inhibitor:	1.0
HLM stability:	0.999 ? 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):

6.541

Half-life (T1/2):

0.216

ADMET: Toxicity

hERG Blockers:	0.167	hERG Blockers (10um):	0.613
Human Hepatotoxicity (H-HT):	0.293	Drug-induced Liver Injury (DILI):	0.165
AMES Toxicity:	0.251	Rat Oral Acute Toxicity:	0.159
Maximum Recommended Daily Dose:	0.16	Skin Sensitization:	0.784
Carcinogencity:	0.481	Eye Corrosion:	0.989
Eye Irritation:	0.995	Respiratory Toxicity:	0.67
Drug-induced Neurotoxicity:	0.223	Ototoxicity:	0.141
Hematotoxicity:	0.17	Drug-induced Nephrotoxicity:	0.27
Genotoxicity:	0.001	RPMI-8226 Immunitoxicity:	0.051
A549 Cytotoxicity:	0.055	Hek293 Cytotoxicity:	0.073
BCF:	1.504 ? 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:	4.017 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.315 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.871 ? 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
NPO60995	Cassia alata	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]

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 NPC510963 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	25181
0.1-0.2	22716
0.2-0.3	1696
0.3-0.4	169
0.4-0.5	59
0.5-0.6	18
0.6-0.7	12
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
0.9643	High Similarity	NPC163345
0.7	Intermediate Similarity	NPC603612
0.6774	Remote Similarity	NPC149299
0.6765	Remote Similarity	NPC223677
0.6667	Remote Similarity	NPC123357
0.6452	Remote Similarity	NPC80396
0.6452	Remote Similarity	NPC154642
0.6	Remote Similarity	NPC250028
0.6	Remote Similarity	NPC236579
0.6	Remote Similarity	NPC80234
0.6	Remote Similarity	NPC226511
0.6	Remote Similarity	NPC203531
0.6	Remote Similarity	NPC256163
0.6	Remote Similarity	NPC40597
0.5938	Remote Similarity	NPC80641
0.5882	Remote Similarity	NPC128061
0.5806	Remote Similarity	NPC223249
0.5806	Remote Similarity	NPC476550
0.5758	Remote Similarity	NPC310746
0.5714	Remote Similarity	NPC71761
0.5625	Remote Similarity	NPC154396
0.5625	Remote Similarity	NPC286695
0.5588	Remote Similarity	NPC15789
0.5455	Remote Similarity	NPC187922
0.5455	Remote Similarity	NPC600941
0.5405	Remote Similarity	NPC10316
0.5405	Remote Similarity	NPC200845
0.5405	Remote Similarity	NPC28779
0.5333	Remote Similarity	NPC53541
0.5312	Remote Similarity	NPC12904
0.5143	Remote Similarity	NPC26253
0.5128	Remote Similarity	NPC277597

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC510963 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6784
0.1-0.2	2210
0.2-0.3	132
0.3-0.4	15
0.4-0.5	8
0.5-0.6	1
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
0.5161	Remote Similarity	NPD900	Pre-clinical

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