NPASS Compound

Natural Product: NPC525020

Natural Product ID	NPC525020
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Decyl butyrate
IUPAC Name	decyl butanoate
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0003909] Fatty Acyls [CHEMONTID:0001722] Fatty alcohol 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 44 43 0 0 0 0 0 0 0 0999 V2000 -5.2556 -1.5951 0.6083 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2887 -1.2271 -0.4751 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4646 0.2016 -0.9409 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2612 1.1928 0.1584 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9011 1.1472 0.7866 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7946 1.4200 -0.1910 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4843 1.3551 0.5186 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7140 1.6088 -0.3340 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8537 0.6250 -1.4677 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9790 -0.7759 -0.9430 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0929 -0.9513 -0.1083 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3955 -0.7391 -0.5236 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5824 -0.3739 -1.6995 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5393 -0.9370 0.3927 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8620 -0.6408 -0.2987 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9458 -0.8809 0.7442 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9972 -1.1844 1.5982 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2684 -1.3392 0.3032 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1976 -2.7165 0.7202 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5352 -1.8732 -1.3632 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2394 -1.4338 -0.2236 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7348 0.4004 -1.7496 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4862 0.3516 -1.3422 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0442 1.0858 0.9297 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4073 2.2070 -0.2827 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7718 0.1137 1.2037 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8514 1.8496 1.6186 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8507 0.8126 -1.0987 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9319 2.4883 -0.5302 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4893 2.1615 1.3076 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3568 0.4099 1.0909 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6124 1.4759 0.3127 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7557 2.6497 -0.7000 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0714 0.6814 -2.0768 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6799 0.9094 -2.1437 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9525 -1.4995 -1.7830 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0732 -0.9822 -0.3351 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4650 -0.2904 1.2912 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5373 -1.9808 0.7658 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9303 0.4301 -0.5773 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9988 -1.2326 -1.2024 H 0 0 0 0 0 0 0 0 0 0 0 0 7.7225 -1.5229 0.2662 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4261 0.0617 1.0691 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5653 -1.4627 1.6102 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 1 0 11 12 1 0 12 13 2 0 12 14 1 0 14 15 1 0 15 16 1 0 1 17 1 0 1 18 1 0 1 19 1 0 2 20 1 0 2 21 1 0 3 22 1 0 3 23 1 0 4 24 1 0 4 25 1 0 5 26 1 0 5 27 1 0 6 28 1 0 6 29 1 0 7 30 1 0 7 31 1 0 8 32 1 0 8 33 1 0 9 34 1 0 9 35 1 0 10 36 1 0 10 37 1 0 14 38 1 0 14 39 1 0 15 40 1 0 15 41 1 0 16 42 1 0 16 43 1 0 16 44 1 0 M END

Standard InCHIKey	PUCQHFICPFUPKW-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C14H28O2/c1-3-5-6-7-8-9-10-11-13-16-14(15)12-4-2/h3-13H2,1-2H3
SMILES	CCCCCCCCCCOC(=O)CCC

Calculated Properties

Physi-Chem Properties

Molecular Weight:	228.21	Volume:	265.644 ? Van der Waals volume.
Dense:	0.859	LogP:	5.633 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.812 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-5.307 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	12.0	Rigid Bonds:	1.0
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:	0.385	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	1.765	Fsp³:	0.929
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:	1
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.016	Fluc inhibitor:	0.032 ? 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:	0.999	Promiscuous compounds:	0.317

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.001	MDCK Permeability:	-4.764
Pgp-inhibitor:	0.005	Pgp-substrate:	0.291
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):	0.143
20% Bioavailability (F20%):	0.544	30% Bioavailability (F30%):	0.481
50% Bioavailability (F50%):	0.842

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.296	MRP1:	0.975
Plasma Protein Binding (PPB):	97.709%	Volume Distribution (VD):	0.471
Fu:	2.45% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.159
OATP1B3 inhibitor:	0.999	BCRP inhibitor:	0.411
BSEP inhibitor:	0.937

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	1.0
CYP2C19-inhibitor:	0.0	CYP2C19-substrate:	0.163
CYP2C9-inhibitor:	0.323	CYP2C9-substrate:	0.599
CYP2D6-inhibitor:	0.077	CYP2D6-substrate:	0.831
CYP3A4-inhibitor:	0.254	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.536	CYP2C8-inhibitor:	1.0
HLM stability:	0.975 ? 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):

5.463

Half-life (T1/2):

0.362

ADMET: Toxicity

hERG Blockers:	0.296	hERG Blockers (10um):	0.724
Human Hepatotoxicity (H-HT):	0.314	Drug-induced Liver Injury (DILI):	0.21
AMES Toxicity:	0.097	Rat Oral Acute Toxicity:	0.202
Maximum Recommended Daily Dose:	0.148	Skin Sensitization:	0.863
Carcinogencity:	0.518	Eye Corrosion:	0.984
Eye Irritation:	0.994	Respiratory Toxicity:	0.706
Drug-induced Neurotoxicity:	0.128	Ototoxicity:	0.153
Hematotoxicity:	0.149	Drug-induced Nephrotoxicity:	0.267
Genotoxicity:	0.0	RPMI-8226 Immunitoxicity:	0.053
A549 Cytotoxicity:	0.133	Hek293 Cytotoxicity:	0.094
BCF:	1.627 ? 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:	4.545 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	5.651 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	4.917 ? 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
NPO16254	Backhousia angustifolia	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO16254	Backhousia angustifolia	Species	Myrtaceae	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 NPC525020 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	26410
0.1-0.2	21387
0.2-0.3	1748
0.3-0.4	221
0.4-0.5	46
0.5-0.6	17
0.6-0.7	9
0.7-0.8	0
0.8-0.85	2
0.85-0.9	1
0.9-0.95	0
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC80641
0.9565	High Similarity	NPC154396
0.88	High Similarity	NPC149299
0.84	Intermediate Similarity	NPC80396
0.8333	Intermediate Similarity	NPC12904
0.7692	Intermediate Similarity	NPC154642
0.7692	Intermediate Similarity	NPC603612
0.76	Intermediate Similarity	NPC223249
0.76	Intermediate Similarity	NPC322892
0.7308	Intermediate Similarity	NPC286695
0.72	Intermediate Similarity	NPC86545
0.72	Intermediate Similarity	NPC286498
0.72	Intermediate Similarity	NPC223374
0.72	Intermediate Similarity	NPC196442
0.72	Intermediate Similarity	NPC301398
0.72	Intermediate Similarity	NPC608162
0.72	Intermediate Similarity	NPC609004
0.6923	Remote Similarity	NPC476550
0.68	Remote Similarity	NPC40965
0.6786	Remote Similarity	NPC223675
0.6786	Remote Similarity	NPC68577
0.6522	Remote Similarity	NPC99700
0.64	Remote Similarity	NPC326758
0.625	Remote Similarity	NPC223677
0.6129	Remote Similarity	NPC71761
0.6071	Remote Similarity	NPC155872
0.5926	Remote Similarity	NPC250028
0.5926	Remote Similarity	NPC236579
0.5926	Remote Similarity	NPC80234
0.5926	Remote Similarity	NPC203531
0.5926	Remote Similarity	NPC256163
0.5926	Remote Similarity	NPC40597
0.5926	Remote Similarity	NPC178643
0.5769	Remote Similarity	NPC248233
0.5769	Remote Similarity	NPC166804
0.5667	Remote Similarity	NPC14608
0.5652	Remote Similarity	NPC327450
0.5652	Remote Similarity	NPC234005
0.5625	Remote Similarity	NPC163345
0.56	Remote Similarity	NPC143211
0.5357	Remote Similarity	NPC147054
0.5185	Remote Similarity	NPC53541
0.5161	Remote Similarity	NPC310746

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC525020 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6734
0.1-0.2	2207
0.2-0.3	169
0.3-0.4	31
0.4-0.5	6
0.5-0.6	0
0.6-0.7	3
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
0.6875	Remote Similarity	NPD631	Phase 4
0.68	Remote Similarity	NPD900	Pre-clinical
0.6667	Remote Similarity	NPD630	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