Natural Product: NPC91263

Natural Product IDNPC91263
Common Name
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The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
AUUYOWKYLNLIJN-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 102420151
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0000134] Phenols
        • [CHEMONTID:0000139] Tyrosols and derivatives

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 AUUYOWKYLNLIJN-UHFFFAOYSA-N
Standard InCHI InChI=1S/C48H88O3/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21-22-23-24-25-26-27-28-29-30-31-32-33-34-35-36-37-38-39-48(50)51-45-44-46-40-42-47(49)43-41-46/h40-43,49H,2-39,44-45H2,1H3
SMILES CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC(=O)OCCc1ccc(cc1)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   712.67 Volume:   846.032
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Van der Waals volume.
Dense:   0.842 LogP:   9.769
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   5.21
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -8.896
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The logarithm of aqueous solubility value.
Rotatable Bonds:   42.0 Rigid Bonds:   7.0
TPSA:   46.53
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Topological Polar Surface Area.
H-Bond Acceptor:   3.0
H-Bond Donor:   1.0 Rings:   1.0
Heavy Atoms:   3.0

MedChem Properties

QED Drug-Likeness Score:   0.054 GASA:   0.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.479 Fsp3:   0.854
MCE-18:   6.0
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MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
Lipinski Rule-of-5:   Accepted
Pfizer Rule:   Accepted GSK Rule:   Accepted
Golden Triangle Rule:   Accepted BMS Rule:   1
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.7 Fluc inhibitor:   0.411
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.0
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.156
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.919 Promiscuous compounds:   0.279

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.131 MDCK Permeability:   -5.051
Pgp-inhibitor:   0.0 Pgp-substrate:   0.013
PAMPA:   0.0
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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):   1.0
20% Bioavailability (F20%):   1.0 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.998
Plasma Protein Binding (PPB):   107.531% Volume Distribution (VD):   3.658
Fu: 0.026%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   0.589
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   1.0
BSEP inhibitor:   0.996

ADMET: Metabolism

CYP1A2-inhibitor:   0.013 CYP1A2-substrate:   1.0
CYP2C19-inhibitor:   0.014 CYP2C19-substrate:   0.999
CYP2C9-inhibitor:   0.639 CYP2C9-substrate:   0.994
CYP2D6-inhibitor:   0.992 CYP2D6-substrate:   0.999
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.002 CYP2C8-inhibitor:   1.0
HLM stability:   0.771
?
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):  3.918 Half-life (T1/2):  7.365

ADMET: Toxicity

hERG Blockers:  0.982 hERG Blockers (10um):  0.994
Human Hepatotoxicity (H-HT):  0.423 Drug-induced Liver Injury (DILI):  0.028
AMES Toxicity:  0.002 Rat Oral Acute Toxicity:  0.023
Maximum Recommended Daily Dose:  0.446 Skin Sensitization:  1.0
Carcinogencity:  0.143 Eye Corrosion:  0.881
Eye Irritation:  0.993 Respiratory Toxicity:  0.995
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  0.077
Hematotoxicity:  0.028 Drug-induced Nephrotoxicity:  0.037
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.025
A549 Cytotoxicity:  0.994 Hek293 Cytotoxicity:  0.484
BCF:   -0.757
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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:   6.154
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   7.993
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   6.499
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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
NPO4756 Mesua elegans Species Calophyllaceae Eukaryota n.a. n.a. n.a. PMID[20943395]
NPO5710 Michelia rajaniana Species Magnoliaceae Eukaryota n.a. n.a. n.a. PMID[3236012]
NPO4756 Mesua elegans Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO81 Erythrina orientalis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4442 Artemisia austriaca Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11244 Chrysolaena propinqua Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25530 Daphne blagayana Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9469 Digitalis obscura Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8378 Fagara heitzii n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO6557 Lotus villosus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28383 Vernonia tufnellae Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5710 Michelia rajaniana Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5060 Onychopetalum amazonicum Species Annonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3215 Phora atra Species Phoridae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO924 Russula subnigricans Species Russulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29440 Sarcomyxa serotina Species Tricholomataceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9318 Stevia serrata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12990 Umbelopsis vinacea Species Umbelopsidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO924 Russula subnigricans Species Russulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9318 Stevia serrata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5710 Michelia rajaniana Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3215 Phora atra Species Phoridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO81 Erythrina orientalis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4442 Artemisia austriaca Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29440 Sarcomyxa serotina Species Tricholomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25530 Daphne blagayana Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9469 Digitalis obscura Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5060 Onychopetalum amazonicum Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6557 Lotus villosus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8378 Fagara heitzii n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO12990 Umbelopsis vinacea Species Umbelopsidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11244 Chrysolaena propinqua Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28383 Vernonia tufnellae Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4756 Mesua elegans Species Calophyllaceae 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 NPC91263 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 NPC31274
0.5714 Remote Similarity NPC323103
0.5577 Remote Similarity NPC484439
0.5227 Remote Similarity NPC604949
0.5094 Remote Similarity NPC142297

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC91263 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