Natural Product: NPC51713

Natural Product IDNPC51713
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 CGXPEDOFBFGHJH-YSPKDNJDSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000513] Eicosanoids
          • [CHEMONTID:0000046] Hydroxyeicosatetraenoic 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 CGXPEDOFBFGHJH-YSPKDNJDSA-N
Standard InCHI InChI=1S/C20H32O4/c1-2-3-4-9-12-15-18(21)19(22)16-13-10-7-5-6-8-11-14-17-20(23)24/h6-8,10,12-13,15-16,18-19,21-22H,2-5,9,11,14,17H2,1H3,(H,23,24)/b8-6-,10-7-,15-12-,16-13+/t18-,19-/m0/s1
SMILES CCCCC/C=C[C@@H]([C@H](/C=C/C=CC/C=CCCCC(=O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   336.23 Volume:   376.455
?
Van der Waals volume.
Dense:   0.893 LogP:   3.776
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.983
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.151
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   14.0 Rigid Bonds:   5.0
TPSA:   77.76
?
Topological Polar Surface Area.
 H-Bond Acceptor:   4.0
H-Bond Donor:   3.0 Rings:   0.0
Heavy Atoms:   4.0

MedChem Properties

QED Drug-Likeness Score:   0.253 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.741 Fsp3:   0.55
MCE-18:   3.0
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Rejected GSK Rule:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.268 Fluc inhibitor:   0.016
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.009
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.005
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.751 Promiscuous compounds:   0.345

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.232 MDCK Permeability:   -5.072
Pgp-inhibitor:   0.001 Pgp-substrate:   0.003
PAMPA:   0.712
?
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):   0.035
20% Bioavailability (F20%):   0.413 30% Bioavailability (F30%):   0.865
50% Bioavailability (F50%):   0.409

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.011 MRP1:   0.976
Plasma Protein Binding (PPB):   92.787% Volume Distribution (VD):   -0.696
Fu: 4.536%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.029
OATP1B3 inhibitor:   0.733 BCRP inhibitor:   0.02
BSEP inhibitor:   0.99

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.001 CYP2C19-substrate:   0.008
CYP2C9-inhibitor:   1.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.001 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.061
CYP2B6-substrate:   0.601 CYP2C8-inhibitor:   0.944
HLM stability:   0.008
?
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):  6.189 Half-life (T1/2):  0.795

ADMET: Toxicity

hERG Blockers:  0.135 hERG Blockers (10um):  0.18
Human Hepatotoxicity (H-HT):  0.18 Drug-induced Liver Injury (DILI):  0.001
AMES Toxicity:  0.475 Rat Oral Acute Toxicity:  0.024
Maximum Recommended Daily Dose:  0.168 Skin Sensitization:  1.0
Carcinogencity:  0.034 Eye Corrosion:  0.156
Eye Irritation:  0.928 Respiratory Toxicity:  0.701
Drug-induced Neurotoxicity:  0.003 Ototoxicity:  0.677
Hematotoxicity:  0.012 Drug-induced Nephrotoxicity:  0.395
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.048
A549 Cytotoxicity:  0.289 Hek293 Cytotoxicity:  0.201
BCF:   0.73
?
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:   3.558
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.828
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.677
?
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
NPO21178 Chloranthus serratus Species Chloranthaceae Eukaryota n.a. n.a. n.a. PMID[19053511]
NPO21178 Chloranthus serratus Species Chloranthaceae Eukaryota n.a. n.a. n.a. PMID[22372956]
NPO21178 Chloranthus serratus Species Chloranthaceae Eukaryota n.a. n.a. n.a. PMID[27588583]
NPO2989 Atalantia monophylla Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[28140592]
NPO21178 Chloranthus serratus Species Chloranthaceae Eukaryota n.a. n.a. n.a. PMID[30724564]
NPO2989 Atalantia monophylla Species Rutaceae Eukaryota Seeds n.a. n.a. PMID[31390210]
NPO2989 Atalantia monophylla Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21178 Chloranthus serratus Species Chloranthaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21178 Chloranthus serratus Species Chloranthaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2989 Atalantia monophylla Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21178 Chloranthus serratus Species Chloranthaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2989 Atalantia monophylla Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21178 Chloranthus serratus Species Chloranthaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21178 Chloranthus serratus Species Chloranthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2989 Atalantia monophylla Species Rutaceae 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 NPC51713 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
0.766 Intermediate Similarity NPC605544
0.766 Intermediate Similarity NPC607260
0.7391 Intermediate Similarity NPC327112
0.7234 Intermediate Similarity NPC323045
0.7234 Intermediate Similarity NPC317881
0.6829 Remote Similarity NPC91495
0.6667 Remote Similarity NPC59051
0.6429 Remote Similarity NPC321062
0.6279 Remote Similarity NPC154245
0.6279 Remote Similarity NPC85813
0.6279 Remote Similarity NPC223697
0.6279 Remote Similarity NPC6095
0.6154 Remote Similarity NPC329249
0.6078 Remote Similarity NPC322461
0.6047 Remote Similarity NPC5413
0.6 Remote Similarity NPC320642
0.5918 Remote Similarity NPC255863
0.5918 Remote Similarity NPC136164
0.5918 Remote Similarity NPC245947
0.5882 Remote Similarity NPC328311
0.58 Remote Similarity NPC321838
0.5686 Remote Similarity NPC325977
0.5686 Remote Similarity NPC329550
0.5682 Remote Similarity NPC70387
0.56 Remote Similarity NPC323597
0.56 Remote Similarity NPC211752
0.56 Remote Similarity NPC323498
0.5581 Remote Similarity NPC424
0.5581 Remote Similarity NPC36061
0.5581 Remote Similarity NPC69510
0.5581 Remote Similarity NPC77272
0.5581 Remote Similarity NPC290563
0.5581 Remote Similarity NPC139029
0.5581 Remote Similarity NPC281972
0.5581 Remote Similarity NPC261831
0.5581 Remote Similarity NPC87564
0.5577 Remote Similarity NPC49863
0.5556 Remote Similarity NPC52955
0.5556 Remote Similarity NPC88966
0.5556 Remote Similarity NPC25417
0.5556 Remote Similarity NPC1813
0.5455 Remote Similarity NPC95145
0.5455 Remote Similarity NPC325642
0.5455 Remote Similarity NPC65174
0.5417 Remote Similarity NPC323436
0.5349 Remote Similarity NPC117572
0.5349 Remote Similarity NPC281245
0.5323 Remote Similarity NPC319021
0.5294 Remote Similarity NPC243532
0.5273 Remote Similarity NPC92558
0.5227 Remote Similarity NPC92114
0.5192 Remote Similarity NPC325627
0.5111 Remote Similarity NPC149821
0.5102 Remote Similarity NPC322002
0.5102 Remote Similarity NPC606120

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC51713 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
0.7391 Intermediate Similarity NPD4246 Phase 2
0.6279 Remote Similarity NPD4266 Phase 2
0.6047 Remote Similarity NPD3173 Phase 4
0.58 Remote Similarity NPD39 Phase 4
0.5581 Remote Similarity NPD3195 Phase 2
0.5581 Remote Similarity NPD3196 Approved
0.5577 Remote Similarity NPD4247 Clinical (unspecified phase)
0.5556 Remote Similarity NPD3172 Approved
0.5417 Remote Similarity NPD3194 Phase 4
0.5349 Remote Similarity NPD4222 Phase 3

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