Natural Product: NPC73436

Natural Product IDNPC73436
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 WJMRPSHNKKDPJZ-AEJSXWLSSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 11030843
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000050] Lactones
        • [CHEMONTID:0001245] Gamma butyrolactones

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 WJMRPSHNKKDPJZ-AEJSXWLSSA-N
Standard InCHI InChI=1S/C11H20O3/c1-3-4-5-6-7-9-10(12)8(2)14-11(9)13/h8-10,12H,3-7H2,1-2H3/t8-,9+,10-/m0/s1
SMILES CCCCCC[C@@H]1[C@H]([C@H](C)OC1=O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   200.14 Volume:   213.99
?
Van der Waals volume.
Dense:   0.935 LogP:   2.402
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.097
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.375
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   5.0 Rigid Bonds:   6.0
TPSA:   46.53
?
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:   0.544 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.359 Fsp3:   0.909
MCE-18:   16.0
?
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:   0.3 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.027
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.004
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.856 Promiscuous compounds:   0.356

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.985 MDCK Permeability:   -4.699
Pgp-inhibitor:   0.042 Pgp-substrate:   0.326
PAMPA:   0.748
?
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):   0.164
20% Bioavailability (F20%):   0.361 30% Bioavailability (F30%):   0.58
50% Bioavailability (F50%):   0.509

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.025 MRP1:   0.865
Plasma Protein Binding (PPB):   84.247% Volume Distribution (VD):   0.337
Fu: 16.862%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.847
OATP1B3 inhibitor:   0.955 BCRP inhibitor:   0.093
BSEP inhibitor:   0.724

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.994
CYP2C19-inhibitor:   0.016 CYP2C19-substrate:   0.134
CYP2C9-inhibitor:   0.065 CYP2C9-substrate:   0.033
CYP2D6-inhibitor:   0.002 CYP2D6-substrate:   0.558
CYP3A4-inhibitor:   0.049 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.976
HLM stability:   0.448
?
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):  3.578 Half-life (T1/2):  1.344

ADMET: Toxicity

hERG Blockers:  0.122 hERG Blockers (10um):  0.499
Human Hepatotoxicity (H-HT):  0.507 Drug-induced Liver Injury (DILI):  0.31
AMES Toxicity:  0.407 Rat Oral Acute Toxicity:  0.31
Maximum Recommended Daily Dose:  0.082 Skin Sensitization:  0.92
Carcinogencity:  0.483 Eye Corrosion:  0.96
Eye Irritation:  0.99 Respiratory Toxicity:  0.578
Drug-induced Neurotoxicity:  0.167 Ototoxicity:  0.258
Hematotoxicity:  0.341 Drug-induced Nephrotoxicity:  0.479
Genotoxicity:  0.006 RPMI-8226 Immunitoxicity:  0.075
A549 Cytotoxicity:  0.297 Hek293 Cytotoxicity:  0.134
BCF:   1.282
?
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:   3.787
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.946
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.379
?
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
NPO24105 Artemisia iwayomogi Species Asteraceae Eukaryota n.a. aerial part n.a. DOI[10.1002/hlca.201300170.]
NPO22210 Allium ampeloprasum Species Amaryllidaceae Eukaryota n.a. n.a. 1996-Sep PMID[10352947]
NPO17888 Myxococcus xanthus Species Myxococcaceae Bacteria n.a. n.a. n.a. PMID[12141877]
NPO24105 Artemisia iwayomogi Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[12735688]
NPO17888 Myxococcus xanthus Species Myxococcaceae Bacteria n.a. n.a. n.a. PMID[14575429]
NPO22210 Allium ampeloprasum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[15877880]
NPO23720 Taxus wallichiana Species Taxaceae Eukaryota needles Himalayan n.a. PMID[16480866]
NPO22210 Allium ampeloprasum Species Amaryllidaceae Eukaryota n.a. Northeastern Regional Plant Introduction Station at Geneva 1966, 1967, and 1968 crop seasons PMID[18460139]
NPO22210 Allium ampeloprasum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO24105 Artemisia iwayomogi Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[23510022]
NPO23720 Taxus wallichiana Species Taxaceae Eukaryota Stem Bark n.a. n.a. PMID[28240909]
NPO23720 Taxus wallichiana Species Taxaceae Eukaryota Roots n.a. n.a. PMID[28581744]
NPO17888 Myxococcus xanthus Species Myxococcaceae Bacteria n.a. n.a. n.a. PMID[31465225]
NPO23720 Taxus wallichiana Species Taxaceae Eukaryota n.a. n.a. n.a. PMID[7264680]
NPO23611 Conyza pallidiflora Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6439 Lithospermum carolinense Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22028 Ligularia lankongensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23781 Lemaireocereus stellatus Species Cactaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18919 Helenium amarum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23113 Garcinia neglecta Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17801 Drimia altissima Species Hyacinthaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21915 Diospyros chloroxylon Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24063 Evasterias retifera Species Asteriidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26544 Bolboschoenus maritimus Species Cyperaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24105 Artemisia iwayomogi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23431 Aconitum umbrosum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19994 Scutellaria viscidula Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17888 Myxococcus xanthus Species Myxococcaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO23175 Streptomyces antibioticus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO22210 Allium ampeloprasum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13151.1 Pulsatilla vulgaris subsp. grandis Subspecies Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21747 Sideritis glacialis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23720 Taxus wallichiana Species Taxaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO21175 Senecio retrorsus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23686 Selinum tenuifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16976 Phebalium rotundifolium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19539 Uperoleia rugosa Species Myobatrachidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23363 Nodulisporium hinnuleum Species Xylariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20290 Vernonia arkansana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9228.2 Narcissus pseudonarcissus subsp. radinganorum Subspecies Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23981 Maytenus disticha Species Celastraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23268 Xanthorrhoea reflexa Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23688 Lonicera nitida Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22210 Allium ampeloprasum Species Amaryllidaceae Eukaryota n.a. n.a. Database[FooDB]
NPO22210 Allium ampeloprasum Species Amaryllidaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO22210 Allium ampeloprasum Species Amaryllidaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO22210 Allium ampeloprasum Species Amaryllidaceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO22210 Allium ampeloprasum Species Amaryllidaceae Eukaryota n.a. n.a. Database[FooDB]
NPO22210 Allium ampeloprasum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18919 Helenium amarum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21175 Senecio retrorsus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19994 Scutellaria viscidula Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23720 Taxus wallichiana Species Taxaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21175 Senecio retrorsus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22210 Allium ampeloprasum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23431 Aconitum umbrosum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18919 Helenium amarum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17801 Drimia altissima Species Hyacinthaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19994 Scutellaria viscidula Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23720 Taxus wallichiana Species Taxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18919 Helenium amarum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19994 Scutellaria viscidula Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23720 Taxus wallichiana Species Taxaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24105 Artemisia iwayomogi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO21175 Senecio retrorsus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23781 Lemaireocereus stellatus Species Cactaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21915 Diospyros chloroxylon Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23688 Lonicera nitida Species Caprifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23363 Nodulisporium hinnuleum Species Xylariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23686 Selinum tenuifolium Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17888 Myxococcus xanthus Species Myxococcaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO22210 Allium ampeloprasum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23611 Conyza pallidiflora Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19994 Scutellaria viscidula Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26544 Bolboschoenus maritimus Species Cyperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24063 Evasterias retifera Species Asteriidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23431 Aconitum umbrosum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19539 Uperoleia rugosa Species Myobatrachidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9228.2 Narcissus pseudonarcissus subsp. radinganorum Subspecies Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22028 Ligularia lankongensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24105 Artemisia iwayomogi Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23268 Xanthorrhoea reflexa Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20290 Vernonia arkansana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23175 Streptomyces antibioticus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO23981 Maytenus disticha Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6439 Lithospermum carolinense Species Boraginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17801 Drimia altissima Species Hyacinthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13151.1 Pulsatilla vulgaris subsp. grandis Subspecies Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18919 Helenium amarum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16976 Phebalium rotundifolium Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23720 Taxus wallichiana Species Taxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21747 Sideritis glacialis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23113 Garcinia neglecta 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

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 NPC73436 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
0.8182 Intermediate Similarity NPC218817
0.8182 Intermediate Similarity NPC11796
0.6923 Remote Similarity NPC228411
0.641 Remote Similarity NPC104926
0.5814 Remote Similarity NPC19136

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC73436 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