Natural Product: NPC182236

Natural Product IDNPC182236
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 UXUPPWPIGVTVQI-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 7775
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

Standard InCHIKey UXUPPWPIGVTVQI-UHFFFAOYSA-N
Standard InCHI InChI=1S/C10H20O2/c1-4-5-6-7-10(11)12-8-9(2)3/h9H,4-8H2,1-3H3
SMILES CCCCCC(=O)OCC(C)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   172.15 Volume:   196.46
?
Van der Waals volume.
Dense:   0.876 LogP:   3.541
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.055
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.159
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   7.0 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:   0.455 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   1.733 Fsp3:   0.9
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:   Rejected
Golden Triangle Rule:   Accepted BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.029 Fluc inhibitor:   0.001
?
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:   0.051

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.612 MDCK Permeability:   -4.549
Pgp-inhibitor:   0.772 Pgp-substrate:   0.25
PAMPA:   0.027
?
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):   0.057
20% Bioavailability (F20%):   0.619 30% Bioavailability (F30%):   0.735
50% Bioavailability (F50%):   0.929

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.079 MRP1:   0.849
Plasma Protein Binding (PPB):   94.595% Volume Distribution (VD):   -0.012
Fu: 5.922%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.739
OATP1B3 inhibitor:   0.434 BCRP inhibitor:   0.032
BSEP inhibitor:   0.998

ADMET: Metabolism

CYP1A2-inhibitor:   0.595 CYP1A2-substrate:   0.986
CYP2C19-inhibitor:   0.95 CYP2C19-substrate:   0.699
CYP2C9-inhibitor:   0.473 CYP2C9-substrate:   0.002
CYP2D6-inhibitor:   0.016 CYP2D6-substrate:   0.8
CYP3A4-inhibitor:   0.996 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.925 CYP2C8-inhibitor:   0.999
HLM stability:   0.996
?
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):  7.325 Half-life (T1/2):  0.272

ADMET: Toxicity

hERG Blockers:  0.127 hERG Blockers (10um):  0.638
Human Hepatotoxicity (H-HT):  0.312 Drug-induced Liver Injury (DILI):  0.196
AMES Toxicity:  0.12 Rat Oral Acute Toxicity:  0.138
Maximum Recommended Daily Dose:  0.16 Skin Sensitization:  0.839
Carcinogencity:  0.514 Eye Corrosion:  0.982
Eye Irritation:  0.993 Respiratory Toxicity:  0.467
Drug-induced Neurotoxicity:  0.128 Ototoxicity:  0.276
Hematotoxicity:  0.243 Drug-induced Nephrotoxicity:  0.395
Genotoxicity:  0.001 RPMI-8226 Immunitoxicity:  0.043
A549 Cytotoxicity:  0.016 Hek293 Cytotoxicity:  0.035
BCF:   0.983
?
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:   3.347
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.158
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.781
?
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 80°N and longitude 4°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 Agrónomos 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]
NPO28968 Teucrium flavum Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[33530639]
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]
NPO28968 Teucrium flavum Species Lamiaceae 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]
NPO28968 Teucrium flavum Species Lamiaceae 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
NPO28968 Teucrium flavum Oil n.a. 0.2 n.a. n.a. % PMID[33530639]

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 NPC182236 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
0.9091 High Similarity NPC81263
0.68 Remote Similarity NPC250028
0.68 Remote Similarity NPC236579
0.68 Remote Similarity NPC80234
0.68 Remote Similarity NPC203531
0.68 Remote Similarity NPC256163
0.68 Remote Similarity NPC40597
0.6552 Remote Similarity NPC308301
0.6071 Remote Similarity NPC80396
0.6071 Remote Similarity NPC154642
0.6071 Remote Similarity NPC600941
0.6071 Remote Similarity NPC603612
0.6 Remote Similarity NPC53541
0.5862 Remote Similarity NPC149299
0.5862 Remote Similarity NPC310746
0.5667 Remote Similarity NPC26253
0.5484 Remote Similarity NPC488257
0.5484 Remote Similarity NPC469937
0.5484 Remote Similarity NPC94699
0.5484 Remote Similarity NPC128061
0.5484 Remote Similarity NPC320588
0.5484 Remote Similarity NPC53463
0.5385 Remote Similarity NPC201622
0.5385 Remote Similarity NPC305660
0.5385 Remote Similarity NPC12156
0.5385 Remote Similarity NPC161097
0.5385 Remote Similarity NPC28598
0.5385 Remote Similarity NPC22903
0.5385 Remote Similarity NPC54980
0.5357 Remote Similarity NPC476550
0.5312 Remote Similarity NPC163345
0.5312 Remote Similarity NPC55678
0.5217 Remote Similarity NPC201132
0.52 Remote Similarity NPC143211
0.5172 Remote Similarity NPC154396
0.5172 Remote Similarity NPC286695

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC182236 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
0.5312 Remote Similarity NPD6125 Phase 4

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