Natural Product: NPC323804

Natural Product IDNPC323804
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 IDEHSDHMEMMYIR-WSAGHCNZSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 16061130
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000513] Eicosanoids
          • [CHEMONTID:0000214] Hydroxyeicosapentaenoic 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 IDEHSDHMEMMYIR-WSAGHCNZSA-N
Standard InCHI InChI=1S/C20H30O3/c1-2-3-4-5-7-10-13-16-19(21)17-14-11-8-6-9-12-15-18-20(22)23/h3-4,6-7,9-11,13-14,16,19,21H,2,5,8,12,15,17-18H2,1H3,(H,22,23)/b4-3-,9-6-,10-7-,14-11-,16-13+
SMILES CCC=CCC=CC=CC(CC=CCC=CCCCC(=O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   318.22 Volume:   365.028
?
Van der Waals volume.
Dense:   0.872 LogP:   4.81
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.878
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.623
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   13.0 Rigid Bonds:   6.0
TPSA:   57.53
?
Topological Polar Surface Area.
 H-Bond Acceptor:   3.0
H-Bond Donor:   2.0 Rings:   0.0
Heavy Atoms:   3.0

MedChem Properties

QED Drug-Likeness Score:   0.286 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.627 Fsp3:   0.45
MCE-18:   2.0
?
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:   0.027 Fluc inhibitor:   0.004
?
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:   0.158
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.951 Promiscuous compounds:   0.065

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.07 MDCK Permeability:   -4.841
Pgp-inhibitor:   0.0 Pgp-substrate:   0.013
PAMPA:   0.909
?
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):   0.072
20% Bioavailability (F20%):   0.103 30% Bioavailability (F30%):   0.719
50% Bioavailability (F50%):   0.335

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.226 MRP1:   0.832
Plasma Protein Binding (PPB):   86.871% Volume Distribution (VD):   -0.667
Fu: 10.814%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.065
OATP1B3 inhibitor:   0.414 BCRP inhibitor:   0.021
BSEP inhibitor:   0.139

ADMET: Metabolism

CYP1A2-inhibitor:   0.002 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.694 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   1.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.102 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.11
CYP2B6-substrate:   1.0 CYP2C8-inhibitor:   0.981
HLM stability:   0.048
?
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):  6.821 Half-life (T1/2):  0.483

ADMET: Toxicity

hERG Blockers:  0.046 hERG Blockers (10um):  0.132
Human Hepatotoxicity (H-HT):  0.291 Drug-induced Liver Injury (DILI):  0.007
AMES Toxicity:  0.511 Rat Oral Acute Toxicity:  0.081
Maximum Recommended Daily Dose:  0.672 Skin Sensitization:  0.976
Carcinogencity:  0.285 Eye Corrosion:  0.011
Eye Irritation:  0.776 Respiratory Toxicity:  0.753
Drug-induced Neurotoxicity:  0.069 Ototoxicity:  0.905
Hematotoxicity:  0.056 Drug-induced Nephrotoxicity:  0.341
Genotoxicity:  0.002 RPMI-8226 Immunitoxicity:  0.026
A549 Cytotoxicity:  0.006 Hek293 Cytotoxicity:  0.055
BCF:   0.529
?
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:   3.266
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.564
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.642
?
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
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[10388717]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[10820136]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[11695850]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[1282214]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[15084647]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[15102880]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[15123652]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[1521032]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. urine n.a. PMID[15239850]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[15466478]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[16538977]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[17190852]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[17499416]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[18039809]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[1814736]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[1928373]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[19572262]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[19662622]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[20951405]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[2188748]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[23384552]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[23723388]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[24085302]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[24096206]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[24343604]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[24503197]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[24814225]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[25070706]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[25727742]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[26041992]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[26485038]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[26608498]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[26654758]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[26676627]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[27466123]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[3025936]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[4002232]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[518564]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[6273168]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[6572072]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[6806263]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[6825837]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[6833497]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[7311739]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[7645303]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[8069858]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[8452569]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[9179722]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[9435160]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[9606952]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[9629662]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[9660093]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. PMID[9694933]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17164 Rattus norvegicus Species Muridae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO17164 Rattus norvegicus Species Muridae 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 NPC323804 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
0.8409 Intermediate Similarity NPC605544
0.8409 Intermediate Similarity NPC607260
0.7333 Intermediate Similarity NPC327112
0.6744 Remote Similarity NPC322002
0.6458 Remote Similarity NPC323045
0.6458 Remote Similarity NPC317881
0.641 Remote Similarity NPC117572
0.6364 Remote Similarity NPC323436
0.6122 Remote Similarity NPC49863
0.6042 Remote Similarity NPC323477
0.5957 Remote Similarity NPC324475
0.5714 Remote Similarity NPC321838
0.56 Remote Similarity NPC322186
0.5581 Remote Similarity NPC70387
0.5577 Remote Similarity NPC328653
0.5455 Remote Similarity NPC52955
0.5455 Remote Similarity NPC88966
0.5455 Remote Similarity NPC25417
0.5455 Remote Similarity NPC1813
0.5349 Remote Similarity NPC149821
0.5294 Remote Similarity NPC325977
0.5227 Remote Similarity NPC91495
0.52 Remote Similarity NPC255863
0.52 Remote Similarity NPC136164
0.52 Remote Similarity NPC245947
0.5192 Remote Similarity NPC328311
0.5192 Remote Similarity NPC26500
0.5111 Remote Similarity NPC59051
0.5094 Remote Similarity NPC322461

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC323804 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
0.7333 Intermediate Similarity NPD4246 Phase 2
0.641 Remote Similarity NPD4222 Phase 3
0.6122 Remote Similarity NPD4247 Clinical (unspecified phase)
0.5455 Remote Similarity NPD3172 Approved
0.5098 Remote Similarity NPD39 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