Natural Product: NPC238577

Natural Product IDNPC238577
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 NHJUPBDCSOGIKX-XEFZRCJWSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 11807209
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000175] Glycerolipids
        • [CHEMONTID:0000637] Glycosylglycerols

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 NHJUPBDCSOGIKX-XEFZRCJWSA-N
Standard InCHI InChI=1S/C9H18O8/c10-1-4(12)3-16-9-8(15)7(14)6(13)5(2-11)17-9/h4-15H,1-3H2/t4-,5+,6-,7-,8+,9+/m0/s1
SMILES C([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:   254.1 Volume:   225.986
?
Van der Waals volume.
Dense:   1.124 LogP:   -1.914
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -1.337
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -0.321
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   5.0 Rigid Bonds:   6.0
TPSA:   139.84
?
Topological Polar Surface Area.
 H-Bond Acceptor:   8.0
H-Bond Donor:   6.0 Rings:   1.0
Heavy Atoms:   8.0

MedChem Properties

QED Drug-Likeness Score:   0.293 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.792 Fsp3:   1.0
MCE-18:   23.0
?
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:   0.166 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.033
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.0
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.424 Promiscuous compounds:   0.024

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.099 MDCK Permeability:   -4.962
Pgp-inhibitor:   0.0 Pgp-substrate:   0.726
PAMPA:   0.997
?
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):   0.921
20% Bioavailability (F20%):   0.858 30% Bioavailability (F30%):   0.969
50% Bioavailability (F50%):   0.921

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.027 MRP1:   0.292
Plasma Protein Binding (PPB):   25.849% Volume Distribution (VD):   -0.533
Fu: 81.701%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.695
OATP1B3 inhibitor:   0.484 BCRP inhibitor:   0.013
BSEP inhibitor:   0.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.077 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.006
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.09
HLM stability:   0.219
?
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):  1.979 Half-life (T1/2):  1.932

ADMET: Toxicity

hERG Blockers:  0.008 hERG Blockers (10um):  0.033
Human Hepatotoxicity (H-HT):  0.432 Drug-induced Liver Injury (DILI):  0.268
AMES Toxicity:  0.985 Rat Oral Acute Toxicity:  0.023
Maximum Recommended Daily Dose:  0.013 Skin Sensitization:  1.0
Carcinogencity:  0.399 Eye Corrosion:  0.008
Eye Irritation:  0.772 Respiratory Toxicity:  0.068
Drug-induced Neurotoxicity:  0.197 Ototoxicity:  0.901
Hematotoxicity:  0.659 Drug-induced Nephrotoxicity:  0.704
Genotoxicity:  0.197 RPMI-8226 Immunitoxicity:  0.089
A549 Cytotoxicity:  0.771 Hek293 Cytotoxicity:  0.303
BCF:   0.004
?
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:   1.044
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   2.202
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   1.479
?
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
NPO2453 Stachybotrys chartarum Species Stachybotryaceae Eukaryota Niphates recondita Weizhou Island, Beibuwan Bay, Guangxi,China n.a. PMID[24387683]
NPO2453 Stachybotrys chartarum Species Stachybotryaceae Eukaryota n.a. n.a. n.a. PMID[24387683]
NPO2453 Stachybotrys chartarum Species Stachybotryaceae Eukaryota n.a. n.a. n.a. PMID[28530828]
NPO2453 Stachybotrys chartarum Species Stachybotryaceae Eukaryota n.a. n.a. n.a. PMID[31265296]
NPO2453 Stachybotrys chartarum Species Stachybotryaceae Eukaryota n.a. n.a. n.a. PMID[32966070]
NPO12586 Tapirira guianensis Species Anacardiaceae Eukaryota n.a. n.a. n.a. PMID[9514013]
NPO9147 Frasera albomarginata Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO31117 Feijoa sellowiana n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO22505 Bombax ceiba Species Malvaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2453 Stachybotrys chartarum Species Stachybotryaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11328 Juniperus chinensis Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28504 Calothrix brevissima Species Rivulariaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO3308 Calycadenia fremontii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12931 Carex pumila Species Cyperaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8395.1 Crepis foetida subsp. rhoeadifolia Subspecies Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13038 Fomes hartigii Species Coriolaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12586 Tapirira guianensis Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8857 Hydnum repandum Species Hydnaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10944 Mantella baroni Species Mantellidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7116 Monachosorum henryi Species Dennstaedtiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2431 Penicilliopsis zonata Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9355 Polygonatum orientale Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9977 Polygonum sieboldi Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12364 Polyides rotundus Species Polyideaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12708 Rothia indica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8225 Salvia karabachensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6781 Senecio acanthifolius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5958 Senegalia modesta Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5472 Spongia foliascens Species Spongiidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO31117 Feijoa sellowiana n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO8225 Salvia karabachensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7116 Monachosorum henryi Species Dennstaedtiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11328 Juniperus chinensis Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8225 Salvia karabachensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22505 Bombax ceiba Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8857 Hydnum repandum Species Hydnaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8225 Salvia karabachensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO31117 Feijoa sellowiana n.a. n.a. n.a. n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9147 Frasera albomarginata Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9355 Polygonatum orientale Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11328 Juniperus chinensis Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22505 Bombax ceiba Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12708 Rothia indica Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13038 Fomes hartigii Species Coriolaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28504 Calothrix brevissima Species Rivulariaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO8857 Hydnum repandum Species Hydnaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6781 Senecio acanthifolius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7116 Monachosorum henryi Species Dennstaedtiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3308 Calycadenia fremontii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5958 Senegalia modesta Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12364 Polyides rotundus Species Polyideaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12931 Carex pumila Species Cyperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8395.1 Crepis foetida subsp. rhoeadifolia Subspecies Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9977 Polygonum sieboldi Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8225 Salvia karabachensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2453 Stachybotrys chartarum Species Stachybotryaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2431 Penicilliopsis zonata Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5472 Spongia foliascens Species Spongiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12586 Tapirira guianensis Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10944 Mantella baroni Species Mantellidae 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 NPC238577 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 NPC326533
0.7941 Intermediate Similarity NPC145112
0.7667 Intermediate Similarity NPC124963
0.6667 Remote Similarity NPC42503
0.6667 Remote Similarity NPC282143
0.6667 Remote Similarity NPC107914
0.6667 Remote Similarity NPC242073
0.6667 Remote Similarity NPC299781
0.6667 Remote Similarity NPC157193
0.6667 Remote Similarity NPC608193
0.6571 Remote Similarity NPC233726
0.6452 Remote Similarity NPC23134
0.6216 Remote Similarity NPC155457
0.5897 Remote Similarity NPC13143
0.5897 Remote Similarity NPC294813
0.5897 Remote Similarity NPC606861
0.5897 Remote Similarity NPC607126
0.5789 Remote Similarity NPC268243
0.5714 Remote Similarity NPC317501
0.5714 Remote Similarity NPC605930
0.5682 Remote Similarity NPC206601
0.561 Remote Similarity NPC89145
0.561 Remote Similarity NPC157514
0.561 Remote Similarity NPC322314
0.561 Remote Similarity NPC269166
0.5556 Remote Similarity NPC143326
0.5476 Remote Similarity NPC100204
0.5405 Remote Similarity NPC31496
0.5349 Remote Similarity NPC36927
0.5349 Remote Similarity NPC262826
0.5349 Remote Similarity NPC271772
0.5294 Remote Similarity NPC323574
0.5227 Remote Similarity NPC147292
0.5227 Remote Similarity NPC150557
0.5208 Remote Similarity NPC488690
0.5128 Remote Similarity NPC130683
0.5122 Remote Similarity NPC603514
0.5111 Remote Similarity NPC306255
0.5111 Remote Similarity NPC277570
0.5111 Remote Similarity NPC63058
0.5106 Remote Similarity NPC12040

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC238577 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
0.7059 Intermediate Similarity NPD904 Phase 3
0.5625 Remote Similarity NPD8994 Approved
0.5556 Remote Similarity NPD905 Phase 4
0.5455 Remote Similarity NPD3181 Phase 3
0.5128 Remote Similarity NPD887 Approved
0.5128 Remote Similarity NPD895 Phase 4

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