Natural Product: NPC92443

Natural Product IDNPC92443
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 KMEKMXBMYZGGDT-OAHLLOKOSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 15569774
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 KMEKMXBMYZGGDT-OAHLLOKOSA-N
Standard InCHI InChI=1S/C16H32O3/c1-2-3-4-5-6-9-12-15(17)13-10-7-8-11-14-16(18)19/h15,17H,2-14H2,1H3,(H,18,19)/p-1/t15-/m1/s1
SMILES CCCCCCCC[C@H](CCCCCCC(=O)[O-])O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   272.24 Volume:   309.026
?
Van der Waals volume.
Dense:   0.881 LogP:   4.642
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.021
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.78
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   14.0 Rigid Bonds:   1.0
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:   0.457 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.379 Fsp3:   0.938
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:   1
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.046 Fluc inhibitor:   0.006
?
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:   0.0
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.99 Promiscuous compounds:   0.581

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.158 MDCK Permeability:   -4.835
Pgp-inhibitor:   0.0 Pgp-substrate:   0.052
PAMPA:   0.818
?
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):   0.655
20% Bioavailability (F20%):   0.552 30% Bioavailability (F30%):   0.941
50% Bioavailability (F50%):   0.506

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.032 MRP1:   0.943
Plasma Protein Binding (PPB):   94.484% Volume Distribution (VD):   -0.03
Fu: 4.361%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.441
OATP1B3 inhibitor:   0.993 BCRP inhibitor:   0.163
BSEP inhibitor:   0.202

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.149
CYP2C19-inhibitor:   0.002 CYP2C19-substrate:   0.049
CYP2C9-inhibitor:   1.0 CYP2C9-substrate:   0.152
CYP2D6-inhibitor:   0.516 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.071 CYP2C8-inhibitor:   0.985
HLM stability:   0.001
?
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):  4.193 Half-life (T1/2):  0.791

ADMET: Toxicity

hERG Blockers:  0.044 hERG Blockers (10um):  0.258
Human Hepatotoxicity (H-HT):  0.545 Drug-induced Liver Injury (DILI):  0.088
AMES Toxicity:  0.052 Rat Oral Acute Toxicity:  0.041
Maximum Recommended Daily Dose:  0.23 Skin Sensitization:  0.943
Carcinogencity:  0.367 Eye Corrosion:  0.978
Eye Irritation:  0.999 Respiratory Toxicity:  0.954
Drug-induced Neurotoxicity:  0.032 Ototoxicity:  0.625
Hematotoxicity:  0.353 Drug-induced Nephrotoxicity:  0.745
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.026
A549 Cytotoxicity:  0.024 Hek293 Cytotoxicity:  0.012
BCF:   1.139
?
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:   3.935
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.239
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   2.9
?
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
NPO19825 Litsea japonica Species Lauraceae Eukaryota leaves n.a. n.a. PMID[14575444]
NPO16934 Nephthea chabrolii Species Nephtheidae Eukaryota n.a. Formosan soft coral n.a. PMID[16309317]
NPO7688 Artemisia selengensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO15450 Minuria leptophylla Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9799 Hebeloma longicaudum Species Cortinariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19234 Hymenopappus newberryi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19565 Crocus chrysanthus Species Iridaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19076 Gaillardia pulchella Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19364 Aconitum chasmanthum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16934 Nephthea chabrolii Species Nephtheidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19076 Gaillardia pulchella Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19364 Aconitum chasmanthum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19364 Aconitum chasmanthum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19076 Gaillardia pulchella Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19076 Gaillardia pulchella Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17577 Azalea ovata n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO15450 Minuria leptophylla Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19825 Litsea japonica Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7688 Artemisia selengensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19364 Aconitum chasmanthum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18518 Haematomma nemetzii Species Haematommataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18499 Podium complanatum Species Sphecidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11060 Doris luteorosea Species Dorididae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9799 Hebeloma longicaudum Species Cortinariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19234 Hymenopappus newberryi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19298 Gerbera crocea Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17341 Gambeya africana n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO16934 Nephthea chabrolii Species Nephtheidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17887 Penstemon centranthifolius Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19696 Othonna quercifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18023 Vitex quinata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21360 Cordia corymbosa Species Cordiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19076 Gaillardia pulchella Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19869 Fusicolla aquaeductuum Species Nectriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19565 Crocus chrysanthus Species Iridaceae 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 NPC92443 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
0.7037 Intermediate Similarity NPC67462
0.7037 Intermediate Similarity NPC156630
0.6176 Remote Similarity NPC324004
0.6176 Remote Similarity NPC328497
0.5758 Remote Similarity NPC262968
0.5278 Remote Similarity NPC255837
0.5278 Remote Similarity NPC224227
0.5143 Remote Similarity NPC184171

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC92443 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
0.7037 Intermediate Similarity NPD3206 Approved
0.5758 Remote Similarity NPD28 Approved
0.5758 Remote Similarity NPD29 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