Natural Product: NPC317381

Natural Product IDNPC317381
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 CDYSHNKYPKNGES-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 14402359
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000262] Fatty acids and conjugates
          • [CHEMONTID:0002949] Long-chain fatty acids

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 CDYSHNKYPKNGES-UHFFFAOYSA-N
Standard InCHI InChI=1S/C14H26O3/c1-2-3-4-5-7-10-13(15)11-8-6-9-12-14(16)17/h2-12H2,1H3,(H,16,17)
SMILES CCCCCCCC(=O)CCCCCC(=O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   242.19 Volume:   271.798
?
Van der Waals volume.
Dense:   0.891 LogP:   4.038
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.989
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.36
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   12.0 Rigid Bonds:   2.0
TPSA:   54.37
?
Topological Polar Surface Area.
 H-Bond Acceptor:   3.0
H-Bond Donor:   1.0 Rings:   0.0
Heavy Atoms:   3.0

MedChem Properties

QED Drug-Likeness Score:   0.527 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   1.869 Fsp3:   0.857
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:   0.004 Fluc inhibitor:   0.019
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.005
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.001
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.996 Promiscuous compounds:   0.72

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.116 MDCK Permeability:   -4.757
Pgp-inhibitor:   0.0 Pgp-substrate:   0.032
PAMPA:   0.907
?
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):   0.405
20% Bioavailability (F20%):   0.111 30% Bioavailability (F30%):   0.119
50% Bioavailability (F50%):   0.06

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.013 MRP1:   0.956
Plasma Protein Binding (PPB):   94.507% Volume Distribution (VD):   -0.0
Fu: 4.522%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.059
OATP1B3 inhibitor:   0.988 BCRP inhibitor:   0.006
BSEP inhibitor:   0.228

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.97
CYP2C19-inhibitor:   0.006 CYP2C19-substrate:   0.866
CYP2C9-inhibitor:   1.0 CYP2C9-substrate:   0.122
CYP2D6-inhibitor:   0.408 CYP2D6-substrate:   0.001
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.868
CYP2B6-substrate:   1.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.02
?
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):  3.784 Half-life (T1/2):  0.584

ADMET: Toxicity

hERG Blockers:  0.086 hERG Blockers (10um):  0.294
Human Hepatotoxicity (H-HT):  0.395 Drug-induced Liver Injury (DILI):  0.143
AMES Toxicity:  0.086 Rat Oral Acute Toxicity:  0.078
Maximum Recommended Daily Dose:  0.178 Skin Sensitization:  0.831
Carcinogencity:  0.236 Eye Corrosion:  0.979
Eye Irritation:  0.996 Respiratory Toxicity:  0.839
Drug-induced Neurotoxicity:  0.078 Ototoxicity:  0.396
Hematotoxicity:  0.331 Drug-induced Nephrotoxicity:  0.444
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.04
A549 Cytotoxicity:  0.01 Hek293 Cytotoxicity:  0.03
BCF:   1.06
?
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:   3.573
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.826
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.139
?
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
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. DOI[10.1042/BA20020118]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. DOI[10.1556/abot.45.2003.3-4.15]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. PMID[15019787]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. PMID[22029392]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. PMID[23517479]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. PMID[37685099]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota Latex Exudate n.a. n.a. Database[FooDB]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. Database[FooDB]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. Database[FooDB]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9498 Papaver somniferum Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9498 Papaver somniferum Species Papaveraceae 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 NPC317381 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 NPC18712
1.0 High Similarity NPC74845
0.7714 Intermediate Similarity NPC477201
0.7576 Intermediate Similarity NPC40082
0.7407 Intermediate Similarity NPC171736
0.7407 Intermediate Similarity NPC301585
0.7407 Intermediate Similarity NPC261080
0.7407 Intermediate Similarity NPC132565
0.7407 Intermediate Similarity NPC209970
0.7407 Intermediate Similarity NPC216630
0.7407 Intermediate Similarity NPC201844
0.7407 Intermediate Similarity NPC301696
0.7407 Intermediate Similarity NPC196924
0.7407 Intermediate Similarity NPC307783
0.7407 Intermediate Similarity NPC154186
0.7407 Intermediate Similarity NPC149184
0.7407 Intermediate Similarity NPC279026
0.7407 Intermediate Similarity NPC113928
0.7407 Intermediate Similarity NPC14227
0.7037 Intermediate Similarity NPC155263
0.6757 Remote Similarity NPC106851
0.6757 Remote Similarity NPC282788
0.6757 Remote Similarity NPC274927
0.641 Remote Similarity NPC251042
0.641 Remote Similarity NPC174447
0.641 Remote Similarity NPC122521
0.6296 Remote Similarity NPC214610
0.6296 Remote Similarity NPC118968
0.6296 Remote Similarity NPC183424
0.6296 Remote Similarity NPC294085
0.6071 Remote Similarity NPC175342
0.6061 Remote Similarity NPC424
0.6061 Remote Similarity NPC36061
0.6061 Remote Similarity NPC69510
0.6061 Remote Similarity NPC77272
0.6061 Remote Similarity NPC8219
0.6061 Remote Similarity NPC290563
0.6061 Remote Similarity NPC139029
0.6061 Remote Similarity NPC281972
0.6061 Remote Similarity NPC261831
0.6061 Remote Similarity NPC87564
0.5926 Remote Similarity NPC268826
0.5882 Remote Similarity NPC95145
0.5882 Remote Similarity NPC325642
0.5882 Remote Similarity NPC65174
0.5758 Remote Similarity NPC281245
0.5714 Remote Similarity NPC87394
0.5714 Remote Similarity NPC235242
0.5714 Remote Similarity NPC324004
0.5714 Remote Similarity NPC328497
0.5714 Remote Similarity NPC602547
0.5625 Remote Similarity NPC55023
0.5625 Remote Similarity NPC21844
0.5588 Remote Similarity NPC129972
0.5588 Remote Similarity NPC301528
0.5588 Remote Similarity NPC71317
0.5588 Remote Similarity NPC92114
0.5588 Remote Similarity NPC163746
0.5588 Remote Similarity NPC103286
0.5556 Remote Similarity NPC225318
0.5556 Remote Similarity NPC174368
0.5556 Remote Similarity NPC154245
0.5556 Remote Similarity NPC85813
0.5556 Remote Similarity NPC223697
0.5556 Remote Similarity NPC6095
0.5484 Remote Similarity NPC604140
0.5357 Remote Similarity NPC134782
0.5357 Remote Similarity NPC79887
0.5357 Remote Similarity NPC606898
0.5349 Remote Similarity NPC325977
0.5349 Remote Similarity NPC143396
0.5294 Remote Similarity NPC314679
0.5278 Remote Similarity NPC321062
0.5152 Remote Similarity NPC180534
0.5152 Remote Similarity NPC611531

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC317381 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
0.7407 Intermediate Similarity NPD2270 Pre-clinical
0.7407 Intermediate Similarity NPD633 Phase 3
0.7407 Intermediate Similarity NPD9448 Phase 2
0.6296 Remote Similarity NPD9655 Phase 4
0.6061 Remote Similarity NPD3195 Phase 2
0.6061 Remote Similarity NPD3196 Approved
0.5714 Remote Similarity NPD3199 Clinical (unspecified phase)
0.5556 Remote Similarity NPD4266 Phase 2
0.5208 Remote Similarity NPD5368 Phase 2
0.5152 Remote Similarity NPD622 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