Natural Product: NPC518369

Natural Product IDNPC518369
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 tridec-6-enyl pentanoate
IUPAC Name tridec-6-enyl pentanoate
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

Standard InCHIKey RXCZMXPOSUQAHS-UHFFFAOYSA-N
Standard InCHI InChI=1S/C18H34O2/c1-3-5-7-8-9-10-11-12-13-14-15-17-20-18(19)16-6-4-2/h10-11H,3-9,12-17H2,1-2H3
SMILES CCCCCCC=CCCCCCOC(=O)CCCC

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   282.26 Volume:   332.192
?
Van der Waals volume.
Dense:   0.85 LogP:   6.764
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.904
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -6.296
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   15.0 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:   0.228 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.107 Fsp3:   0.833
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:   0.077 Fluc inhibitor:   0.198
?
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:   0.004
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.997 Promiscuous compounds:   0.538

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.018 MDCK Permeability:   -4.703
Pgp-inhibitor:   0.184 Pgp-substrate:   0.298
PAMPA:   0.003
?
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):   0.213
20% Bioavailability (F20%):   0.769 30% Bioavailability (F30%):   0.84
50% Bioavailability (F50%):   0.734

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.317 MRP1:   0.963
Plasma Protein Binding (PPB):   98.342% Volume Distribution (VD):   -0.249
Fu: 1.05%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.055
OATP1B3 inhibitor:   0.983 BCRP inhibitor:   0.532
BSEP inhibitor:   0.997

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   1.0
CYP2C19-inhibitor:   0.058 CYP2C19-substrate:   0.998
CYP2C9-inhibitor:   0.424 CYP2C9-substrate:   0.048
CYP2D6-inhibitor:   0.001 CYP2D6-substrate:   1.0
CYP3A4-inhibitor:   0.152 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.045 CYP2C8-inhibitor:   1.0
HLM stability:   0.951
?
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):  5.5 Half-life (T1/2):  0.33

ADMET: Toxicity

hERG Blockers:  0.446 hERG Blockers (10um):  0.728
Human Hepatotoxicity (H-HT):  0.161 Drug-induced Liver Injury (DILI):  0.006
AMES Toxicity:  0.087 Rat Oral Acute Toxicity:  0.087
Maximum Recommended Daily Dose:  0.097 Skin Sensitization:  0.999
Carcinogencity:  0.163 Eye Corrosion:  0.999
Eye Irritation:  0.997 Respiratory Toxicity:  0.457
Drug-induced Neurotoxicity:  0.015 Ototoxicity:  0.112
Hematotoxicity:  0.019 Drug-induced Nephrotoxicity:  0.41
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.057
A549 Cytotoxicity:  0.373 Hek293 Cytotoxicity:  0.169
BCF:   1.502
?
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:   4.502
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.75
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.658
?
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
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota Seeds n.a. n.a. PMID[28134521]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[32415726]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[37667613]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[37917799]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[38005226]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[38067590]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[39588261]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota n.a. n.a. Database[FooDB]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota n.a. n.a. Database[FooDB]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota Stem Bark n.a. n.a. Database[FooDB]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota Bark n.a. n.a. Database[FooDB]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9138 Syzygium cumini Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9138 Syzygium cumini 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
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 NPC518369 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.5 or Top200).

Similarity Score Similarity Level Natural Product ID
0.8438 Intermediate Similarity NPC223677
0.8387 Intermediate Similarity NPC71761
0.7419 Intermediate Similarity NPC149299
0.7097 Intermediate Similarity NPC80396
0.7097 Intermediate Similarity NPC80641
0.697 Remote Similarity NPC128061
0.6774 Remote Similarity NPC154396
0.6774 Remote Similarity NPC286695
0.6562 Remote Similarity NPC154642
0.6562 Remote Similarity NPC603612
0.6471 Remote Similarity NPC207815
0.6452 Remote Similarity NPC223249
0.6452 Remote Similarity NPC476550
0.6389 Remote Similarity NPC28779
0.6053 Remote Similarity NPC277597
0.5938 Remote Similarity NPC322892
0.5938 Remote Similarity NPC12904
0.5897 Remote Similarity NPC104537
0.5882 Remote Similarity NPC309606
0.5833 Remote Similarity NPC163345
0.5625 Remote Similarity NPC86545
0.5625 Remote Similarity NPC286498
0.5625 Remote Similarity NPC223374
0.5625 Remote Similarity NPC196442
0.5625 Remote Similarity NPC301398
0.5625 Remote Similarity NPC608162
0.5625 Remote Similarity NPC609004
0.561 Remote Similarity NPC475443
0.561 Remote Similarity NPC473829
0.5526 Remote Similarity NPC10316
0.5526 Remote Similarity NPC200845
0.5476 Remote Similarity NPC330426
0.5476 Remote Similarity NPC127091
0.5476 Remote Similarity NPC22101
0.5429 Remote Similarity NPC223675
0.5429 Remote Similarity NPC68577
0.5405 Remote Similarity NPC39633
0.5349 Remote Similarity NPC54925
0.5312 Remote Similarity NPC40965
0.5238 Remote Similarity NPC143857
0.5238 Remote Similarity NPC321919
0.5238 Remote Similarity NPC229252
0.5238 Remote Similarity NPC476654
0.5238 Remote Similarity NPC476655
0.5238 Remote Similarity NPC476656
0.5227 Remote Similarity NPC48218
0.5227 Remote Similarity NPC141481
0.5227 Remote Similarity NPC464342
0.5152 Remote Similarity NPC250028
0.5152 Remote Similarity NPC236579
0.5152 Remote Similarity NPC80234
0.5152 Remote Similarity NPC203531
0.5152 Remote Similarity NPC256163
0.5152 Remote Similarity NPC40597
0.5135 Remote Similarity NPC228473
0.5094 Remote Similarity NPC470237

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC518369 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
0.5641 Remote Similarity NPD631 Phase 4
0.55 Remote Similarity NPD630 Approved
0.5312 Remote Similarity NPD900 Pre-clinical

Bioactivity similarity

  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