Natural Product: NPC255707

Natural Product IDNPC255707
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 JEVVKJMRZMXFBT-NUJKBMONSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 6325554
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001554] Tetraterpenoids
          • [CHEMONTID:0001277] Carotenoids
            • [CHEMONTID:0001410] Xanthophylls

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 JEVVKJMRZMXFBT-NUJKBMONSA-N
Standard InCHI InChI=1S/C40H56O2/c1-33(19-11-21-35(3)23-13-25-37(5)27-15-29-39(7)31-41)17-9-10-18-34(2)20-12-22-36(4)24-14-26-38(6)28-16-30-40(8)32-42/h9-14,17-26,29-30,41-42H,15-16,27-28,31-32H2,1-8H3/b10-9+,19-11-,20-12+,23-13-,24-14+,33-17-,34-18+,35-21-,36-22?,37-25-,38-26?,39-29-,40-30+
SMILES C/C(=C/C=C/C=C(C)/C=C/C=C(C)/C=C/C=C(C)CC/C=C(C)/CO)/C=CC=C(C)/C=CC=C(C)/CC/C=C(/C)CO

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   568.43 Volume:   683.702
?
Van der Waals volume.
Dense:   0.831 LogP:   9.053
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   5.928
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -6.227
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   18.0 Rigid Bonds:   13.0
TPSA:   40.46
?
Topological Polar Surface Area.
 H-Bond Acceptor:   2.0
H-Bond Donor:   2.0 Rings:   0.0
Heavy Atoms:   2.0

MedChem Properties

QED Drug-Likeness Score:   0.127 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.777 Fsp3:   0.35
MCE-18:   0.0
?
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:   1.0 Fluc inhibitor:   0.461
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.0
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.007
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.667 Promiscuous compounds:   0.108

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.682 MDCK Permeability:   -4.717
Pgp-inhibitor:   0.956 Pgp-substrate:   0.965
PAMPA:   0.111
?
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):   0.002
20% Bioavailability (F20%):   0.472 30% Bioavailability (F30%):   0.943
50% Bioavailability (F50%):   0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.989
Plasma Protein Binding (PPB):   93.141% Volume Distribution (VD):   0.183
Fu: 6.633%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   0.636 BCRP inhibitor:   0.003
BSEP inhibitor:   1.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.001 CYP1A2-substrate:   0.06
CYP2C19-inhibitor:   0.001 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.628 CYP2C9-substrate:   0.019
CYP2D6-inhibitor:   0.978 CYP2D6-substrate:   0.003
CYP3A4-inhibitor:   0.005 CYP3A4-substrate:   0.997
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
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):  8.339 Half-life (T1/2):  0.586

ADMET: Toxicity

hERG Blockers:  0.227 hERG Blockers (10um):  0.527
Human Hepatotoxicity (H-HT):  0.83 Drug-induced Liver Injury (DILI):  0.001
AMES Toxicity:  0.326 Rat Oral Acute Toxicity:  0.117
Maximum Recommended Daily Dose:  0.74 Skin Sensitization:  1.0
Carcinogencity:  0.491 Eye Corrosion:  0.0
Eye Irritation:  0.48 Respiratory Toxicity:  0.632
Drug-induced Neurotoxicity:  0.119 Ototoxicity:  0.756
Hematotoxicity:  0.11 Drug-induced Nephrotoxicity:  0.868
Genotoxicity:  0.009 RPMI-8226 Immunitoxicity:  0.084
A549 Cytotoxicity:  0.026 Hek293 Cytotoxicity:  0.491
BCF:   2.369
?
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:   5.264
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.619
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   6.167
?
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
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. DOI[10.1016/0045-6535(91)90110-Y]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.abb.2017.09.009]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jfca.2004.07.004]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jfca.2005.08.001]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jfca.2005.08.001]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. retail stores, supermarkets and market stalls in Forssa and in the Helsinki area 2003–2005 DOI[10.1016/j.jfca.2006.05.007]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. retail stores, supermarkets and market stalls in Forssa and in the Helsinki area 2003–2005 DOI[10.1016/j.jfca.2006.05.007]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jplph.2011.12.019]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/S0885-5765(05)80069-4]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. DOI[10.1093/jxb/erx356]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. 1996-Sep PMID[10352947]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. 1996-Sep PMID[10352947]
NPO683 Rosa canina Species Rosaceae Eukaryota n.a. n.a. n.a. PMID[12880322]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. Himeji City, Japan n.a. PMID[15053555]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[15877880]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[15877880]
NPO8182 Momordica charantia Species Cucurbitaceae Eukaryota n.a. n.a. n.a. PMID[17685651]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[17764147]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. Northeastern Regional Plant Introduction Station at Geneva 1966, 1967, and 1968 crop seasons PMID[18460139]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. Northeastern Regional Plant Introduction Station at Geneva 1966, 1967, and 1968 crop seasons PMID[18460139]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO8182 Momordica charantia Species Cucurbitaceae Eukaryota Stems n.a. n.a. PMID[18637688]
NPO18296 Diospyros kaki Species Ebenaceae Eukaryota n.a. calyx n.a. PMID[21561086]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[21800857]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. exocarp n.a. PMID[21800857]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. root n.a. PMID[21800857]
NPO18296 Diospyros kaki Species Ebenaceae Eukaryota n.a. fruit n.a. PMID[24086493]
NPO8182 Momordica charantia Species Cucurbitaceae Eukaryota Roots n.a. n.a. PMID[24836069]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[2831703]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[2831703]
NPO8182 Momordica charantia Species Cucurbitaceae Eukaryota n.a. n.a. n.a. PMID[28621938]
NPO8182 Momordica charantia Species Cucurbitaceae Eukaryota Vines n.a. n.a. PMID[32357011]
NPO18296 Diospyros kaki Species Ebenaceae Eukaryota n.a. n.a. n.a. PMID[37324556]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[37980871]
NPO8182 Momordica charantia Species Cucurbitaceae Eukaryota n.a. n.a. n.a. PMID[38440938]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[6821187]
NPO12948 Solanum dulcamara Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18296 Diospyros kaki Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8182 Momordica charantia Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7273 Brassica rutabaga Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO683 Rosa canina Species Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO163 Daucus carota Species Apiaceae Eukaryota Roots n.a. Database[FooDB]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. Database[FooDB]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO163 Daucus carota Species Apiaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO8182 Momordica charantia Species Cucurbitaceae Eukaryota n.a. n.a. Database[FooDB]
NPO163 Daucus carota Species Apiaceae Eukaryota Tissue Culture n.a. n.a. Database[FooDB]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO163 Daucus carota Species Apiaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO163 Daucus carota Species Apiaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. Database[FooDB]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO8182 Momordica charantia Species Cucurbitaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO163 Daucus carota Species Apiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO8182 Momordica charantia Species Cucurbitaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO8182 Momordica charantia Species Cucurbitaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO163 Daucus carota Species Apiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO163 Daucus carota Species Apiaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO18296 Diospyros kaki Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12948 Solanum dulcamara Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8182 Momordica charantia Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO683 Rosa canina Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7273 Brassica rutabaga Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO8182 Momordica charantia Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7273 Brassica rutabaga Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12948 Solanum dulcamara Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO683 Rosa canina Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18296 Diospyros kaki Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18296 Diospyros kaki Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO31303 Solanum lycopersicum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12948 Solanum dulcamara Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO683 Rosa canina Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8182 Momordica charantia Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO163 Daucus carota Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18296 Diospyros kaki Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7273 Brassica rutabaga Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO683 Rosa canina Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12948 Solanum dulcamara Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8182 Momordica charantia Species Cucurbitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18296 Diospyros kaki Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO163 Daucus carota Species Apiaceae 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 NPC255707 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
0.7097 Intermediate Similarity NPC99088
0.7097 Intermediate Similarity NPC173592
0.5143 Remote Similarity NPC116934
0.5128 Remote Similarity NPC138935
0.5106 Remote Similarity NPC604204

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC255707 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