Natural Product: NPC244149

Natural Product IDNPC244149
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 KVQVGSDBGJXNGV-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 15264
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002837] Hydrocarbons
      • [CHEMONTID:0004474] Saturated hydrocarbons
        • [CHEMONTID:0002500] Alkanes
          • [CHEMONTID:0004620] Branched alkanes

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 KVQVGSDBGJXNGV-UHFFFAOYSA-N
Standard InCHI InChI=1S/C19H40/c1-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19(2)3/h19H,4-18H2,1-3H3
SMILES CCCCCCCCCCCCCCCCC(C)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   268.31 Volume:   337.18
?
Van der Waals volume.
Dense:   0.796 LogP:   8.845
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   4.703
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -9.049
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   15.0 Rigid Bonds:   0.0
TPSA:   0.0
?
Topological Polar Surface Area.
 H-Bond Acceptor:   0.0
H-Bond Donor:   0.0 Rings:   0.0
Heavy Atoms:   0.0

MedChem Properties

QED Drug-Likeness Score:   0.269 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   1.581 Fsp3:   1.0
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:   Rejected BMS Rule:   1
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.66 Fluc inhibitor:   0.458
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.001
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.001
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.998 Promiscuous compounds:   0.218

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.057 MDCK Permeability:   -4.854
Pgp-inhibitor:   0.004 Pgp-substrate:   0.013
PAMPA:   0.0
?
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):   0.49
20% Bioavailability (F20%):   0.743 30% Bioavailability (F30%):   0.985
50% Bioavailability (F50%):   0.946

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.211 MRP1:   0.967
Plasma Protein Binding (PPB):   101.609% Volume Distribution (VD):   1.871
Fu: 0.513%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.387
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.92
BSEP inhibitor:   0.171

ADMET: Metabolism

CYP1A2-inhibitor:   0.02 CYP1A2-substrate:   0.994
CYP2C19-inhibitor:   0.78 CYP2C19-substrate:   0.465
CYP2C9-inhibitor:   0.978 CYP2C9-substrate:   0.727
CYP2D6-inhibitor:   0.966 CYP2D6-substrate:   0.234
CYP3A4-inhibitor:   0.101 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.998 CYP2C8-inhibitor:   0.998
HLM stability:   0.461
?
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):  5.499 Half-life (T1/2):  0.634

ADMET: Toxicity

hERG Blockers:  0.549 hERG Blockers (10um):  0.899
Human Hepatotoxicity (H-HT):  0.515 Drug-induced Liver Injury (DILI):  0.086
AMES Toxicity:  0.082 Rat Oral Acute Toxicity:  0.188
Maximum Recommended Daily Dose:  0.243 Skin Sensitization:  0.985
Carcinogencity:  0.347 Eye Corrosion:  0.996
Eye Irritation:  0.998 Respiratory Toxicity:  0.958
Drug-induced Neurotoxicity:  0.031 Ototoxicity:  0.176
Hematotoxicity:  0.201 Drug-induced Nephrotoxicity:  0.109
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.053
A549 Cytotoxicity:  0.809 Hek293 Cytotoxicity:  0.12
BCF:   1.107
?
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:   5.019
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.065
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   6.051
?
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
NPO6947 Astilbe chinensis Species Saxifragaceae Eukaryota rhizomes n.a. n.a. PMID[19585998]
NPO30614 Forsythia koreana Species Oleaceae Eukaryota n.a. n.a. n.a. PMID[37354439]
NPO6947 Astilbe chinensis Species Saxifragaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO30614 Forsythia koreana Species Oleaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6947 Astilbe chinensis Species Saxifragaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30614 Forsythia koreana Species Oleaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6947 Astilbe chinensis Species Saxifragaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6947 Astilbe chinensis Species Saxifragaceae 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
NPO30614 Forsythia koreana Oil Flowers 1.02 n.a. n.a. % PMID[37354439]

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 NPC244149 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
0.6667 Remote Similarity NPC27501
0.6154 Remote Similarity NPC605142
0.5833 Remote Similarity NPC273385
0.5833 Remote Similarity NPC278711
0.5833 Remote Similarity NPC98925
0.5833 Remote Similarity NPC64370
0.5833 Remote Similarity NPC82648
0.5833 Remote Similarity NPC110911
0.5833 Remote Similarity NPC227986
0.5833 Remote Similarity NPC239406
0.5833 Remote Similarity NPC77249
0.5833 Remote Similarity NPC26974
0.5833 Remote Similarity NPC136996
0.5833 Remote Similarity NPC302327
0.5833 Remote Similarity NPC154477
0.5833 Remote Similarity NPC89422
0.5833 Remote Similarity NPC26229
0.5625 Remote Similarity NPC172053
0.5333 Remote Similarity NPC14312
0.5263 Remote Similarity NPC69245
0.5263 Remote Similarity NPC221022

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC244149 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