Natural Product: NPC294423

Natural Product IDNPC294423
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 PADHSFRQMFRWLS-BFQBLSCMSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 15589787
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000175] Glycerolipids
        • [CHEMONTID:0000637] Glycosylglycerols
          • [CHEMONTID:0003819] Glycosylmonoradylglycerols
            • [CHEMONTID:0001773] Glycosylmonoacylglycerols

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 PADHSFRQMFRWLS-BFQBLSCMSA-N
Standard InCHI InChI=1S/C18H24O10/c19-7-13-15(23)16(24)17(25)18(28-13)27-9-12(21)8-26-14(22)6-3-10-1-4-11(20)5-2-10/h1-6,12-13,15-21,23-25H,7-9H2/b6-3+/t12-,13-,15-,16+,17-,18-/m1/s1
SMILES c1cc(ccc1/C=C/C(=O)OC[C@H](CO[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   400.14 Volume:   377.491
?
Van der Waals volume.
Dense:   1.06 LogP:   -0.079
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.576
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.152
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   9.0 Rigid Bonds:   14.0
TPSA:   166.14
?
Topological Polar Surface Area.
 H-Bond Acceptor:   10.0
H-Bond Donor:   6.0 Rings:   2.0
Heavy Atoms:   10.0

MedChem Properties

QED Drug-Likeness Score:   0.215 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.854 Fsp3:   0.5
MCE-18:   50.556
?
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:   Accepted
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.686 Fluc inhibitor:   0.65
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.333
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.212
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.27 Promiscuous compounds:   0.345

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.347 MDCK Permeability:   -5.146
Pgp-inhibitor:   0.0 Pgp-substrate:   0.084
PAMPA:   0.998
?
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):   0.084
20% Bioavailability (F20%):   0.832 30% Bioavailability (F30%):   0.983
50% Bioavailability (F50%):   0.992

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.001 MRP1:   0.001
Plasma Protein Binding (PPB):   69.618% Volume Distribution (VD):   -0.351
Fu: 30.614%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.009
BSEP inhibitor:   0.04

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.005
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.007
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.001
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.008
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.038
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.45
?
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):  2.19 Half-life (T1/2):  2.179

ADMET: Toxicity

hERG Blockers:  0.049 hERG Blockers (10um):  0.145
Human Hepatotoxicity (H-HT):  0.528 Drug-induced Liver Injury (DILI):  0.683
AMES Toxicity:  0.83 Rat Oral Acute Toxicity:  0.009
Maximum Recommended Daily Dose:  0.102 Skin Sensitization:  1.0
Carcinogencity:  0.222 Eye Corrosion:  0.0
Eye Irritation:  0.2 Respiratory Toxicity:  0.008
Drug-induced Neurotoxicity:  0.085 Ototoxicity:  0.919
Hematotoxicity:  0.088 Drug-induced Nephrotoxicity:  0.652
Genotoxicity:  0.421 RPMI-8226 Immunitoxicity:  0.048
A549 Cytotoxicity:  0.253 Hek293 Cytotoxicity:  0.318
BCF:   0.384
?
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:   2.939
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.47
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.736
?
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
NPO14775 Eupenicillium javanicum Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[17711347]
NPO14775 Eupenicillium javanicum Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[18771240]
NPO3457 Streptomyces diastaticus Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[8904845]
NPO20448 Trifolium caucasicum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5811 Pityrodia lepidota Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14775 Eupenicillium javanicum Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16807 Cyclamen purpurascens Species Primulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4414 Lilium lancifolium Species Liliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3457 Streptomyces diastaticus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO7907 Lilium pumilum Species Liliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16807 Cyclamen purpurascens Species Primulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7907 Lilium pumilum Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4414 Lilium lancifolium Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4414 Lilium lancifolium Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7907 Lilium pumilum Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO1475 Lilium brownii Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4414 Lilium lancifolium Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20448 Trifolium caucasicum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1475 Lilium brownii Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5811 Pityrodia lepidota Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7907 Lilium pumilum Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14775 Eupenicillium javanicum Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16807 Cyclamen purpurascens Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20313 Crotalus mitchellii Species Viperidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4414 Lilium lancifolium Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19342 Bryocladia cuspidata Species Rhodomelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3457 Streptomyces diastaticus Species Streptomycetaceae Bacteria 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 NPC294423 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 NPC52097
0.7636 Intermediate Similarity NPC11724
0.6842 Remote Similarity NPC313193
0.6667 Remote Similarity NPC477293
0.6333 Remote Similarity NPC232880
0.625 Remote Similarity NPC225307
0.6081 Remote Similarity NPC28637
0.6029 Remote Similarity NPC288416
0.5942 Remote Similarity NPC477294
0.5921 Remote Similarity NPC476869
0.5921 Remote Similarity NPC476866
0.5844 Remote Similarity NPC254819
0.5797 Remote Similarity NPC479473
0.5797 Remote Similarity NPC275721
0.5797 Remote Similarity NPC479468
0.5797 Remote Similarity NPC479474
0.5758 Remote Similarity NPC157554
0.5753 Remote Similarity NPC252114
0.5694 Remote Similarity NPC34293
0.5625 Remote Similarity NPC202391
0.5625 Remote Similarity NPC296659
0.5541 Remote Similarity NPC145319
0.5493 Remote Similarity NPC229784
0.5455 Remote Similarity NPC476867
0.541 Remote Similarity NPC157338
0.5375 Remote Similarity NPC204644
0.5333 Remote Similarity NPC166180
0.5325 Remote Similarity NPC281798
0.5294 Remote Similarity NPC307110
0.5294 Remote Similarity NPC3460
0.5273 Remote Similarity NPC304638
0.525 Remote Similarity NPC49597
0.525 Remote Similarity NPC46644
0.5246 Remote Similarity NPC306255
0.5217 Remote Similarity NPC253668
0.5217 Remote Similarity NPC57039
0.5217 Remote Similarity NPC83218
0.5217 Remote Similarity NPC479471
0.5217 Remote Similarity NPC126991
0.5217 Remote Similarity NPC479467
0.5217 Remote Similarity NPC201249
0.5217 Remote Similarity NPC479470
0.5217 Remote Similarity NPC479472
0.5211 Remote Similarity NPC470572
0.519 Remote Similarity NPC476864
0.5185 Remote Similarity NPC96599
0.5152 Remote Similarity NPC476872
0.5143 Remote Similarity NPC184633
0.5143 Remote Similarity NPC202700
0.5135 Remote Similarity NPC291153
0.5132 Remote Similarity NPC219677
0.5122 Remote Similarity NPC31745
0.5122 Remote Similarity NPC479970
0.5122 Remote Similarity NPC220936
0.5122 Remote Similarity NPC12006
0.5077 Remote Similarity NPC601241
0.5077 Remote Similarity NPC606576
0.5062 Remote Similarity NPC471881
0.5062 Remote Similarity NPC205195
0.5062 Remote Similarity NPC476868
0.5057 Remote Similarity NPC184464
0.5057 Remote Similarity NPC251062
0.5057 Remote Similarity NPC119537
0.5056 Remote Similarity NPC28651

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC294423 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