Natural Product: NPC479053

Natural Product IDNPC479053
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 CNAXYMJHMHYJAV-SFQUDFHCSA-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]

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 CNAXYMJHMHYJAV-SFQUDFHCSA-N
Standard InCHI InChI=1S/C23H26O3/c1-16(2)8-7-9-17(3)12-13-20-21(24)14-19(15-22(20)25)23(26)18-10-5-4-6-11-18/h4-6,8,10-12,14-15,24-25H,7,9,13H2,1-3H3/b17-12+
SMILES CC(=CCC/C(=C/Cc1c(cc(cc1O)C(=O)c1ccccc1)O)/C)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   350.19 Volume:   391.894
?
Van der Waals volume.
Dense:   0.894 LogP:   5.64
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   4.246
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.747
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   7.0 Rigid Bonds:   15.0
TPSA:   57.53
?
Topological Polar Surface Area.
 H-Bond Acceptor:   3.0
H-Bond Donor:   2.0 Rings:   2.0
Heavy Atoms:   3.0

MedChem Properties

QED Drug-Likeness Score:   0.507 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.536 Fsp3:   0.261
MCE-18:   14.0
?
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:   0.94 Fluc inhibitor:   0.224
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.506
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.464
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.647 Promiscuous compounds:   0.082

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.206 MDCK Permeability:   -4.771
Pgp-inhibitor:   0.954 Pgp-substrate:   0.001
PAMPA:   0.029
?
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):   0.0
20% Bioavailability (F20%):   0.015 30% Bioavailability (F30%):   0.034
50% Bioavailability (F50%):   0.851

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.005 MRP1:   0.765
Plasma Protein Binding (PPB):   97.373% Volume Distribution (VD):   0.269
Fu: 2.454%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.999
OATP1B3 inhibitor:   0.99 BCRP inhibitor:   0.03
BSEP inhibitor:   0.969

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.994
CYP2C19-inhibitor:   0.023 CYP2C19-substrate:   1.0
CYP2C9-inhibitor:   0.065 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.004 CYP2D6-substrate:   0.783
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.937
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.908
?
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):  7.855 Half-life (T1/2):  1.041

ADMET: Toxicity

hERG Blockers:  0.182 hERG Blockers (10um):  0.651
Human Hepatotoxicity (H-HT):  0.816 Drug-induced Liver Injury (DILI):  0.772
AMES Toxicity:  0.21 Rat Oral Acute Toxicity:  0.449
Maximum Recommended Daily Dose:  0.531 Skin Sensitization:  0.979
Carcinogencity:  0.154 Eye Corrosion:  0.0
Eye Irritation:  0.908 Respiratory Toxicity:  0.984
Drug-induced Neurotoxicity:  0.317 Ototoxicity:  0.502
Hematotoxicity:  0.268 Drug-induced Nephrotoxicity:  0.692
Genotoxicity:  0.759 RPMI-8226 Immunitoxicity:  0.228
A549 Cytotoxicity:  0.561 Hek293 Cytotoxicity:  0.622
BCF:   2.024
?
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:   5.003
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.541
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   6.055
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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
NPO19087 Garcinia kola Species Clusiaceae Eukaryota Seeds n.a. n.a. PMID[32644811]
NPO19087 Garcinia kola Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19087 Garcinia kola Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19087 Garcinia kola Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19087 Garcinia kola Species Clusiaceae 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
NPT1127 Organism Porphyromonas gingivalis Porphyromonas gingivalis MIC = 62500.0 nM PMID[32644811]
NPT1127 Organism Porphyromonas gingivalis Porphyromonas gingivalis MBC > 1000.0 uM PMID[32644811]
NPT1483 Organism Streptococcus sobrinus Streptococcus sobrinus MIC = 15600.0 nM PMID[32644811]
NPT1483 Organism Streptococcus sobrinus Streptococcus sobrinus MBC = 31.3 uM PMID[32644811]

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 NPC479053 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 NPC105157
0.6786 Remote Similarity NPC602136
0.6667 Remote Similarity NPC102384
0.6538 Remote Similarity NPC33728
0.6538 Remote Similarity NPC488443
0.6 Remote Similarity NPC12640
0.566 Remote Similarity NPC201662
0.5636 Remote Similarity NPC606098
0.5536 Remote Similarity NPC144343
0.5455 Remote Similarity NPC99836
0.537 Remote Similarity NPC91105
0.5345 Remote Similarity NPC483761
0.5345 Remote Similarity NPC166995
0.5312 Remote Similarity NPC118919
0.5312 Remote Similarity NPC488439
0.5312 Remote Similarity NPC292894
0.5312 Remote Similarity NPC230334
0.5273 Remote Similarity NPC263753
0.5238 Remote Similarity NPC608784
0.5167 Remote Similarity NPC24125
0.5161 Remote Similarity NPC139074
0.5085 Remote Similarity NPC39029
0.5085 Remote Similarity NPC600345
0.5082 Remote Similarity NPC124269

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC479053 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
NPD

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