Natural Product: NPC179037

Natural Product IDNPC179037
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 PKRPFNXROFUNDE-NSHDSACASA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 5315583
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000145] Coumarins and derivatives
        • [CHEMONTID:0000358] Furanocoumarins
          • [CHEMONTID:0002569] Linear furanocoumarins
            • [CHEMONTID:0000202] Psoralens
              • [CHEMONTID:0002832] 5-methoxypsoralens

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 PKRPFNXROFUNDE-NSHDSACASA-N
Standard InCHI InChI=1S/C17H18O7/c1-17(2,20)11(18)8-23-16-14-10(6-7-22-14)13(21-3)9-4-5-12(19)24-15(9)16/h4-7,11,18,20H,8H2,1-3H3/t11-/m0/s1
SMILES CC(C)([C@H](COc1c2c(cco2)c(c2ccc(=O)oc12)OC)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   334.11 Volume:   322.632
?
Van der Waals volume.
Dense:   1.036 LogP:   1.308
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.647
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.6
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   5.0 Rigid Bonds:   16.0
TPSA:   102.27
?
Topological Polar Surface Area.
 H-Bond Acceptor:   7.0
H-Bond Donor:   2.0 Rings:   3.0
Heavy Atoms:   7.0

MedChem Properties

QED Drug-Likeness Score:   0.688 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.365 Fsp3:   0.353
MCE-18:   40.0
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Rejected GSK Rule:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.24 Fluc inhibitor:   0.125
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.859
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.07
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.054 Promiscuous compounds:   0.322

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.5 MDCK Permeability:   -4.562
Pgp-inhibitor:   0.002 Pgp-substrate:   0.005
PAMPA:   0.588
?
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):   0.004
20% Bioavailability (F20%):   0.592 30% Bioavailability (F30%):   0.331
50% Bioavailability (F50%):   0.665

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.014 MRP1:   0.928
Plasma Protein Binding (PPB):   72.514% Volume Distribution (VD):   -0.135
Fu: 25.329%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.999
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.004
BSEP inhibitor:   0.858

ADMET: Metabolism

CYP1A2-inhibitor:   0.092 CYP1A2-substrate:   0.003
CYP2C19-inhibitor:   0.007 CYP2C19-substrate:   0.001
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.07
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.925
CYP3A4-inhibitor:   0.037 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.978
HLM stability:   0.004
?
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):  9.253 Half-life (T1/2):  1.005

ADMET: Toxicity

hERG Blockers:  0.076 hERG Blockers (10um):  0.238
Human Hepatotoxicity (H-HT):  0.516 Drug-induced Liver Injury (DILI):  0.659
AMES Toxicity:  0.586 Rat Oral Acute Toxicity:  0.311
Maximum Recommended Daily Dose:  0.706 Skin Sensitization:  0.517
Carcinogencity:  0.798 Eye Corrosion:  0.004
Eye Irritation:  0.617 Respiratory Toxicity:  0.421
Drug-induced Neurotoxicity:  0.228 Ototoxicity:  0.469
Hematotoxicity:  0.388 Drug-induced Nephrotoxicity:  0.341
Genotoxicity:  0.968 RPMI-8226 Immunitoxicity:  0.061
A549 Cytotoxicity:  0.076 Hek293 Cytotoxicity:  0.315
BCF:   0.463
?
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:   3.055
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.54
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.856
?
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
NPO3854 Ruta graveolens Species Rutaceae Eukaryota n.a. n.a. n.a. DOI[10.1042/BA20070200]
NPO24758 Angelica dahurica Species Apiaceae Eukaryota n.a. root n.a. DOI[10.5012/bkcs.2003.24.11.1699]
NPO24758 Angelica dahurica Species Apiaceae Eukaryota n.a. root n.a. PMID[12510838]
NPO3854 Ruta graveolens Species Rutaceae Eukaryota leaves n.a. n.a. PMID[12568545]
NPO18674 Juglans regia Species Juglandaceae Eukaryota n.a. root n.a. PMID[14727919]
NPO18674 Juglans regia Species Juglandaceae Eukaryota n.a. leaf n.a. PMID[14727919]
NPO18674 Juglans regia Species Juglandaceae Eukaryota n.a. xylem n.a. PMID[14727919]
NPO18674 Juglans regia Species Juglandaceae Eukaryota n.a. bark n.a. PMID[14727919]
NPO11147 Spongia hispida Species Spongiidae Eukaryota n.a. n.a. n.a. PMID[1479380]
NPO24758 Angelica dahurica Species Apiaceae Eukaryota n.a. root n.a. PMID[15646793]
NPO22063 Solanum lycocarpum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[17249729]
NPO18674 Juglans regia Species Juglandaceae Eukaryota n.a. pericarp n.a. PMID[18496782]
NPO3854 Ruta graveolens Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[19191562]
NPO24758 Angelica dahurica Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[21625478]
NPO24758 Angelica dahurica Species Apiaceae Eukaryota n.a. root n.a. PMID[21657081]
NPO8874 Glehnia littoralis Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[24813739]
NPO18674 Juglans regia Species Juglandaceae Eukaryota n.a. n.a. n.a. PMID[25466114]
NPO24758 Angelica dahurica Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[27444348]
NPO3854 Ruta graveolens Species Rutaceae Eukaryota Whole Plants n.a. n.a. PMID[28093914]
NPO18674 Juglans regia Species Juglandaceae Eukaryota Flowers n.a. n.a. PMID[28737396]
NPO24758 Angelica dahurica Species Apiaceae Eukaryota Roots n.a. n.a. PMID[31464439]
NPO18674 Juglans regia Species Juglandaceae Eukaryota n.a. n.a. n.a. PMID[36431782]
NPO18674 Juglans regia Species Juglandaceae Eukaryota n.a. n.a. n.a. PMID[37570937]
NPO18674 Juglans regia Species Juglandaceae Eukaryota n.a. leaf n.a. Database[Article]
NPO5835 Heracleum granatense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22063 Solanum lycocarpum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1141 Citrus sp. Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4849 Peucedanum stenocarpum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8874 Glehnia littoralis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3854 Ruta graveolens Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29004 Ruta pinnata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18674 Juglans regia Species Juglandaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18674 Juglans regia Species Juglandaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO18674 Juglans regia Species Juglandaceae Eukaryota Testa n.a. n.a. Database[FooDB]
NPO18674 Juglans regia Species Juglandaceae Eukaryota Stem Bark n.a. n.a. Database[FooDB]
NPO18674 Juglans regia Species Juglandaceae Eukaryota Embryo n.a. n.a. Database[FooDB]
NPO18674 Juglans regia Species Juglandaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO18674 Juglans regia Species Juglandaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO18674 Juglans regia Species Juglandaceae Eukaryota n.a. n.a. Database[FooDB]
NPO4849 Peucedanum stenocarpum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28681 Angelica glabra Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16910 Peucedanum grande Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28975 Thamnosma rhodesica Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8874 Glehnia littoralis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18674 Juglans regia Species Juglandaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5835 Heracleum granatense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO31235 Citrus sp Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29004 Ruta pinnata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24758 Angelica dahurica Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3854 Ruta graveolens Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24758 Angelica dahurica Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28975 Thamnosma rhodesica Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29004 Ruta pinnata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28681 Angelica glabra Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3854 Ruta graveolens Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15022 Baccharis flabellata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23289.1 Heracleum sphondylium subsp. pyrenaicum Subspecies Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8874 Glehnia littoralis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16910 Peucedanum grande Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18674 Juglans regia Species Juglandaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5835 Heracleum granatense Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1141 Citrus sp. Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4849 Peucedanum stenocarpum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18674 Juglans regia Species Juglandaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3854 Ruta graveolens Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24758 Angelica dahurica Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8874 Glehnia littoralis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8874 Glehnia littoralis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18674 Juglans regia Species Juglandaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO24758 Angelica dahurica Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO24758 Angelica dahurica Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14231 Senecio barba-johannis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16778 Leptospermum liversidgei Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28681 Angelica glabra Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8874 Glehnia littoralis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15022 Baccharis flabellata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28975 Thamnosma rhodesica Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15484 Adlumia fungosa Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22063 Solanum lycocarpum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23289.1 Heracleum sphondylium subsp. pyrenaicum Subspecies Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11147 Spongia hispida Species Spongiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19012 Gasteria bicolor Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18926 Tephrosia lupinifolia Species Geometridae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29004 Ruta pinnata Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18674 Juglans regia Species Juglandaceae 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 NPC179037 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 NPC224165
0.8214 Intermediate Similarity NPC107244
0.8103 Intermediate Similarity NPC198876
0.8 Intermediate Similarity NPC478570
0.7705 Intermediate Similarity NPC478569
0.7308 Intermediate Similarity NPC234536
0.7302 Intermediate Similarity NPC53917
0.7288 Intermediate Similarity NPC144288
0.7119 Intermediate Similarity NPC210460
0.678 Remote Similarity NPC51404
0.678 Remote Similarity NPC83421
0.6557 Remote Similarity NPC67450
0.6462 Remote Similarity NPC478566
0.6393 Remote Similarity NPC155264
0.6176 Remote Similarity NPC193881
0.6129 Remote Similarity NPC303210
0.6129 Remote Similarity NPC95472
0.6129 Remote Similarity NPC239270
0.6056 Remote Similarity NPC478568
0.5882 Remote Similarity NPC478567
0.5469 Remote Similarity NPC215722
0.5167 Remote Similarity NPC487850
0.5156 Remote Similarity NPC479800
0.5077 Remote Similarity NPC600693
0.5077 Remote Similarity NPC605376
0.5072 Remote Similarity NPC190970

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC179037 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