Natural Product: NPC116610

Natural Product IDNPC116610
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 GZZPOFFXKUVNSW-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 125207
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000262] Fatty acids and conjugates
          • [CHEMONTID:0003086] Medium-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 GZZPOFFXKUVNSW-UHFFFAOYSA-N
Standard InCHI InChI=1S/C12H22O2/c1-2-3-4-5-6-7-8-9-10-11-12(13)14/h2H,1,3-11H2,(H,13,14)
SMILES C=CCCCCCCCCCC(=O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   198.16 Volume:   228.416
?
Van der Waals volume.
Dense:   0.868 LogP:   4.376
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.883
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.639
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   10.0 Rigid Bonds:   2.0
TPSA:   37.3
?
Topological Polar Surface Area.
 H-Bond Acceptor:   2.0
H-Bond Donor:   1.0 Rings:   0.0
Heavy Atoms:   2.0

MedChem Properties

QED Drug-Likeness Score:   0.428 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   1.906 Fsp3:   0.75
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:   Accepted BMS Rule:   1
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.005 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:   0.998 Promiscuous compounds:   0.763

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.068 MDCK Permeability:   -4.716
Pgp-inhibitor:   0.001 Pgp-substrate:   0.001
PAMPA:   0.568
?
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):   0.14
20% Bioavailability (F20%):   0.211 30% Bioavailability (F30%):   0.502
50% Bioavailability (F50%):   0.209

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.162 MRP1:   0.935
Plasma Protein Binding (PPB):   97.838% Volume Distribution (VD):   -0.402
Fu: 1.26%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.515
OATP1B3 inhibitor:   0.973 BCRP inhibitor:   0.218
BSEP inhibitor:   0.118

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.044
CYP2C19-inhibitor:   0.011 CYP2C19-substrate:   0.197
CYP2C9-inhibitor:   1.0 CYP2C9-substrate:   0.085
CYP2D6-inhibitor:   0.139 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.964
CYP2B6-substrate:   0.982 CYP2C8-inhibitor:   0.992
HLM stability:   0.004
?
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):  3.723 Half-life (T1/2):  0.782

ADMET: Toxicity

hERG Blockers:  0.038 hERG Blockers (10um):  0.246
Human Hepatotoxicity (H-HT):  0.25 Drug-induced Liver Injury (DILI):  0.113
AMES Toxicity:  0.155 Rat Oral Acute Toxicity:  0.172
Maximum Recommended Daily Dose:  0.19 Skin Sensitization:  0.957
Carcinogencity:  0.414 Eye Corrosion:  0.989
Eye Irritation:  0.998 Respiratory Toxicity:  0.731
Drug-induced Neurotoxicity:  0.126 Ototoxicity:  0.271
Hematotoxicity:  0.198 Drug-induced Nephrotoxicity:  0.116
Genotoxicity:  0.001 RPMI-8226 Immunitoxicity:  0.028
A549 Cytotoxicity:  0.018 Hek293 Cytotoxicity:  0.015
BCF:   1.309
?
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:   3.788
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.118
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.408
?
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
NPO5716 Mallotus nudiflorus Species Euphorbiaceae Eukaryota n.a. bark n.a. DOI[10.1002/hlca.200590219]
NPO30645 Poria cocos Species Coriolaceae Eukaryota n.a. sclerotium n.a. PMID[21250700]
NPO2601 Ovis aries Species Bovidae Eukaryota n.a. n.a. n.a. PMID[24937646]
NPO7776 Pithomyces chartarum Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9335 Gomophia watsoni n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO3823 Helichrysum stirlingii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9582 Ormocarpum kirkii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7397 Tephrosia obovata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO30645 Poria cocos Species Coriolaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10253 Pithecellobium dulce Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7776 Pithomyces chartarum Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2601 Ovis aries Species Bovidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30645 Poria cocos Species Coriolaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2601 Ovis aries Species Bovidae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO2601 Ovis aries Species Bovidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24974 Zingiber montanum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7776 Pithomyces chartarum Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO30645 Poria cocos Species Coriolaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2601 Ovis aries Species Bovidae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7196 Jaborosa parviflora Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2858 Ercolania funerea Species Limapontiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9335 Gomophia watsoni n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO7776 Pithomyces chartarum Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7397 Tephrosia obovata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8629 Ruppia maritima Species Cymodoceaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5716 Mallotus nudiflorus Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9982 Heptacyclum zenkeri n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO10253 Pithecellobium dulce Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24974 Zingiber montanum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1277 Pamburus missionis Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3823 Helichrysum stirlingii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2601 Ovis aries Species Bovidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5840 Stellaria heterophylla Species Caryophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9582 Ormocarpum kirkii Species Fabaceae 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 NPC116610 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 NPC180534
1.0 High Similarity NPC611531
0.7391 Intermediate Similarity NPC214610
0.7391 Intermediate Similarity NPC118968
0.7391 Intermediate Similarity NPC183424
0.7391 Intermediate Similarity NPC294085
0.7143 Intermediate Similarity NPC34416
0.7143 Intermediate Similarity NPC281245
0.6957 Remote Similarity NPC268826
0.6897 Remote Similarity NPC424
0.6897 Remote Similarity NPC36061
0.6897 Remote Similarity NPC69510
0.6897 Remote Similarity NPC77272
0.6897 Remote Similarity NPC290563
0.6897 Remote Similarity NPC139029
0.6897 Remote Similarity NPC281972
0.6897 Remote Similarity NPC261831
0.6897 Remote Similarity NPC87564
0.6667 Remote Similarity NPC95145
0.6667 Remote Similarity NPC325642
0.6667 Remote Similarity NPC65174
0.6538 Remote Similarity NPC171736
0.6538 Remote Similarity NPC301585
0.6538 Remote Similarity NPC261080
0.6538 Remote Similarity NPC132565
0.6538 Remote Similarity NPC209970
0.6538 Remote Similarity NPC216630
0.6538 Remote Similarity NPC201844
0.6538 Remote Similarity NPC301696
0.6538 Remote Similarity NPC196924
0.6538 Remote Similarity NPC307783
0.6538 Remote Similarity NPC154186
0.6538 Remote Similarity NPC149184
0.6538 Remote Similarity NPC279026
0.6538 Remote Similarity NPC113928
0.6538 Remote Similarity NPC14227
0.6333 Remote Similarity NPC92114
0.6296 Remote Similarity NPC604140
0.625 Remote Similarity NPC52955
0.625 Remote Similarity NPC88966
0.625 Remote Similarity NPC25417
0.625 Remote Similarity NPC134782
0.625 Remote Similarity NPC1813
0.625 Remote Similarity NPC154245
0.625 Remote Similarity NPC85813
0.625 Remote Similarity NPC223697
0.625 Remote Similarity NPC6095
0.6176 Remote Similarity NPC18357
0.6154 Remote Similarity NPC155263
0.6129 Remote Similarity NPC207292
0.5938 Remote Similarity NPC321062
0.5938 Remote Similarity NPC70387
0.5862 Remote Similarity NPC55023
0.5862 Remote Similarity NPC21844
0.5769 Remote Similarity NPC175342
0.5758 Remote Similarity NPC174560
0.5758 Remote Similarity NPC125312
0.5667 Remote Similarity NPC50457
0.5667 Remote Similarity NPC604910
0.5556 Remote Similarity NPC225929
0.5556 Remote Similarity NPC606120
0.5526 Remote Similarity NPC485704
0.5484 Remote Similarity NPC314679
0.5455 Remote Similarity NPC5413
0.5455 Remote Similarity NPC602547
0.5417 Remote Similarity NPC18224
0.5312 Remote Similarity NPC8219
0.5294 Remote Similarity NPC59051
0.5263 Remote Similarity NPC106851
0.5263 Remote Similarity NPC282788
0.5263 Remote Similarity NPC274927
0.5263 Remote Similarity NPC477201
0.525 Remote Similarity NPC68343
0.525 Remote Similarity NPC54766
0.525 Remote Similarity NPC328089
0.52 Remote Similarity NPC174368
0.5152 Remote Similarity NPC18712
0.5152 Remote Similarity NPC149821
0.5152 Remote Similarity NPC74845
0.5135 Remote Similarity NPC487561
0.5128 Remote Similarity NPC179764

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC116610 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
1.0 High Similarity NPD622 Pre-clinical
0.7391 Intermediate Similarity NPD9655 Phase 4
0.6897 Remote Similarity NPD3195 Phase 2
0.6897 Remote Similarity NPD3196 Approved
0.6538 Remote Similarity NPD2270 Pre-clinical
0.6538 Remote Similarity NPD633 Phase 3
0.6538 Remote Similarity NPD9448 Phase 2
0.625 Remote Similarity NPD3172 Approved
0.625 Remote Similarity NPD4266 Phase 2
0.5556 Remote Similarity NPD3194 Phase 4
0.5455 Remote Similarity NPD3173 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