Natural Product: NPC313030

Natural Product IDNPC313030
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 (14'z)-5-(Nonadeca-14'-Enyl)Resorcinol
IUPAC Name 5-[(Z)-nonadec-14-enyl]benzene-1,3-diol
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL1795550
PubChem CID 53357972
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0000134] Phenols
        • [CHEMONTID:0001286] Benzenediols
          • [CHEMONTID:0000137] Resorcinols

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 KEAYVGHLOUCYNN-WAYWQWQTSA-N
Standard InCHI InChI=1S/C25H42O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-23-20-24(26)22-25(27)21-23/h5-6,20-22,26-27H,2-4,7-19H2,1H3/b6-5-
SMILES CCCC/C=CCCCCCCCCCCCCCc1cc(cc(c1)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   374.32 Volume:   439.434
?
Van der Waals volume.
Dense:   0.852 LogP:   10.049
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   5.419
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -6.729
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   17.0 Rigid Bonds:   7.0
TPSA:   40.46
?
Topological Polar Surface Area.
 H-Bond Acceptor:   2.0
H-Bond Donor:   2.0 Rings:   1.0
Heavy Atoms:   2.0

MedChem Properties

QED Drug-Likeness Score:   0.214 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.362 Fsp3:   0.68
MCE-18:   6.0
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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:   Accepted BMS Rule:   1
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.736 Fluc inhibitor:   0.351
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.002
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.052
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.934 Promiscuous compounds:   0.083

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.261 MDCK Permeability:   -4.731
Pgp-inhibitor:   0.517 Pgp-substrate:   0.0
PAMPA:   0.0
?
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):   0.002
20% Bioavailability (F20%):   0.812 30% Bioavailability (F30%):   0.951
50% Bioavailability (F50%):   0.988

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.044 MRP1:   0.93
Plasma Protein Binding (PPB):   99.012% Volume Distribution (VD):   0.71
Fu: 0.313%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.099
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.948
BSEP inhibitor:   0.997

ADMET: Metabolism

CYP1A2-inhibitor:   0.017 CYP1A2-substrate:   0.999
CYP2C19-inhibitor:   0.43 CYP2C19-substrate:   0.997
CYP2C9-inhibitor:   1.0 CYP2C9-substrate:   0.997
CYP2D6-inhibitor:   1.0 CYP2D6-substrate:   0.999
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.004 CYP2C8-inhibitor:   1.0
HLM stability:   0.873
?
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):  4.001 Half-life (T1/2):  1.353

ADMET: Toxicity

hERG Blockers:  0.804 hERG Blockers (10um):  0.938
Human Hepatotoxicity (H-HT):  0.222 Drug-induced Liver Injury (DILI):  0.001
AMES Toxicity:  0.088 Rat Oral Acute Toxicity:  0.073
Maximum Recommended Daily Dose:  0.481 Skin Sensitization:  1.0
Carcinogencity:  0.045 Eye Corrosion:  0.991
Eye Irritation:  0.998 Respiratory Toxicity:  0.889
Drug-induced Neurotoxicity:  0.004 Ototoxicity:  0.077
Hematotoxicity:  0.003 Drug-induced Nephrotoxicity:  0.128
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.063
A549 Cytotoxicity:  0.985 Hek293 Cytotoxicity:  0.914
BCF:   1.042
?
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:   5.183
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.317
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.938
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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
NPO33268 wheat n.a. n.a. n.a. wheat germ n.a. n.a. PMID[19284743]
NPO33268 wheat n.a. n.a. n.a. wheat bran n.a. n.a. PMID[21658963]
NPO33268 wheat n.a. n.a. n.a. 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
NPT393 Cell line HCT-116 Homo sapiens IC50 = 17.65 ug.mL-1 DrugMatrix in vivo data: Pathology

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 NPC313030 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
1.0 High Similarity NPC53051
1.0 High Similarity NPC24404
0.9697 High Similarity NPC146798
0.9697 High Similarity NPC222522
0.9697 High Similarity NPC106396
0.9697 High Similarity NPC94351
0.9697 High Similarity NPC168303
0.9375 High Similarity NPC470700
0.9375 High Similarity NPC54844
0.9375 High Similarity NPC39097
0.9375 High Similarity NPC302681
0.9375 High Similarity NPC118286
0.9375 High Similarity NPC109691
0.8889 High Similarity NPC71002
0.8889 High Similarity NPC302219
0.8889 High Similarity NPC249828
0.8824 High Similarity NPC39664
0.8378 Intermediate Similarity NPC242342
0.8378 Intermediate Similarity NPC85479
0.7895 Intermediate Similarity NPC10588
0.7879 Intermediate Similarity NPC294186
0.7879 Intermediate Similarity NPC147310
0.7879 Intermediate Similarity NPC137415
0.7879 Intermediate Similarity NPC166313
0.7879 Intermediate Similarity NPC192032
0.7879 Intermediate Similarity NPC24407
0.7879 Intermediate Similarity NPC11280
0.7692 Intermediate Similarity NPC72947
0.7632 Intermediate Similarity NPC166761
0.75 Intermediate Similarity NPC246056
0.7442 Intermediate Similarity NPC305603
0.7436 Intermediate Similarity NPC284011
0.7179 Intermediate Similarity NPC483454
0.7179 Intermediate Similarity NPC162314
0.7045 Intermediate Similarity NPC61033
0.7 Intermediate Similarity NPC94139
0.7 Intermediate Similarity NPC147284
0.6923 Remote Similarity NPC232523
0.675 Remote Similarity NPC488413
0.675 Remote Similarity NPC488412
0.6667 Remote Similarity NPC127894
0.6667 Remote Similarity NPC470759
0.6512 Remote Similarity NPC210497
0.65 Remote Similarity NPC486908
0.6458 Remote Similarity NPC123559
0.6458 Remote Similarity NPC140521
0.6429 Remote Similarity NPC158253
0.6316 Remote Similarity NPC241891
0.6316 Remote Similarity NPC134829
0.6222 Remote Similarity NPC470760
0.6098 Remote Similarity NPC487734
0.6 Remote Similarity NPC483450
0.5854 Remote Similarity NPC55561
0.5814 Remote Similarity NPC129373
0.5814 Remote Similarity NPC488416
0.5778 Remote Similarity NPC192
0.5778 Remote Similarity NPC219070
0.5778 Remote Similarity NPC483449
0.575 Remote Similarity NPC487946
0.575 Remote Similarity NPC487945
0.5714 Remote Similarity NPC196479
0.5682 Remote Similarity NPC204901
0.5625 Remote Similarity NPC249836
0.561 Remote Similarity NPC177420
0.55 Remote Similarity NPC3358
0.55 Remote Similarity NPC306884
0.55 Remote Similarity NPC603092
0.5435 Remote Similarity NPC48730
0.5417 Remote Similarity NPC486909
0.54 Remote Similarity NPC17840
0.54 Remote Similarity NPC470699
0.54 Remote Similarity NPC247477
0.5385 Remote Similarity NPC59506
0.5333 Remote Similarity NPC114064
0.5306 Remote Similarity NPC15860
0.525 Remote Similarity NPC488411
0.525 Remote Similarity NPC488410
0.525 Remote Similarity NPC488409
0.5227 Remote Similarity NPC487735
0.5128 Remote Similarity NPC123273
0.5128 Remote Similarity NPC318325
0.5116 Remote Similarity NPC280347
0.5111 Remote Similarity NPC115808

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC313030 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
NPD

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