Natural Product: NPC34910

Natural Product IDNPC34910
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
Oxalicumone D
IUPAC Name (2R,4S)-2,4-dihydroxy-4-[(2S)-5-hydroxy-7-methyl-4-oxo-2,3-dihydrothieno[2,3-b]chromen-2-yl]-5-methoxy-5-oxopentanoic acid
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL3263077
PubChem CID 90676612
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000123] Benzopyrans
        • [CHEMONTID:0003410] 1-benzopyrans
          • [CHEMONTID:0000144] Chromones

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 ROHDJYQMXQAIJT-GDAOTKPNSA-N
Standard InCHI InChI=1S/C18H18O9S/c1-7-3-9(19)13-11(4-7)27-16-8(14(13)21)5-12(28-16)18(25,17(24)26-2)6-10(20)15(22)23/h3-4,10,12,19-20,25H,5-6H2,1-2H3,(H,22,23)/t10-,12+,18-/m1/s1
SMILES Cc1cc(c2c(c1)oc1c(C[C@@H]([C@](C[C@H](C(=O)O)O)(C(=O)OC)O)S1)c2=O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   410.07 Volume:   373.381
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Van der Waals volume.
Dense:   1.098 LogP:   1.876
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.907
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -2.624
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The logarithm of aqueous solubility value.
Rotatable Bonds:   6.0 Rigid Bonds:   18.0
TPSA:   154.5
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Topological Polar Surface Area.
H-Bond Acceptor:   9.0
H-Bond Donor:   4.0 Rings:   3.0
Heavy Atoms:   10.0

MedChem Properties

QED Drug-Likeness Score:   0.514 GASA:   1.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.473 Fsp3:   0.389
MCE-18:   72.68
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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:   0.389 Fluc inhibitor:   0.123
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.168
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.261
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.525 Promiscuous compounds:   0.195

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.426 MDCK Permeability:   -4.917
Pgp-inhibitor:   0.0 Pgp-substrate:   0.747
PAMPA:   0.996
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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):   0.0
20% Bioavailability (F20%):   0.026 30% Bioavailability (F30%):   0.15
50% Bioavailability (F50%):   0.99

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.048 MRP1:   0.996
Plasma Protein Binding (PPB):   94.935% Volume Distribution (VD):   -0.282
Fu: 3.757%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   0.974
OATP1B3 inhibitor:   0.831 BCRP inhibitor:   0.011
BSEP inhibitor:   0.52

ADMET: Metabolism

CYP1A2-inhibitor:   0.018 CYP1A2-substrate:   0.002
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.919 CYP2C9-substrate:   0.001
CYP2D6-inhibitor:   0.969 CYP2D6-substrate:   0.111
CYP3A4-inhibitor:   0.001 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.002
HLM stability:   0.688
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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):  2.039 Half-life (T1/2):  2.03

ADMET: Toxicity

hERG Blockers:  0.007 hERG Blockers (10um):  0.033
Human Hepatotoxicity (H-HT):  0.597 Drug-induced Liver Injury (DILI):  0.764
AMES Toxicity:  0.258 Rat Oral Acute Toxicity:  0.312
Maximum Recommended Daily Dose:  0.799 Skin Sensitization:  0.865
Carcinogencity:  0.347 Eye Corrosion:  0.018
Eye Irritation:  0.605 Respiratory Toxicity:  0.679
Drug-induced Neurotoxicity:  0.012 Ototoxicity:  0.425
Hematotoxicity:  0.256 Drug-induced Nephrotoxicity:  0.8
Genotoxicity:  0.951 RPMI-8226 Immunitoxicity:  0.085
A549 Cytotoxicity:  0.045 Hek293 Cytotoxicity:  0.075
BCF:   0.581
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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:   3.318
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.8
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.025
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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
NPO12404 Trigonostemon chinensis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[18611050]
NPO33528 Penicillium oxalicum SCSGAF 0023 Species Aspergillaceae Eukaryota isolated from gorgonian Muricella flexuosa South China Sea, Sanya (1811N, 10925E), Hainan Province, China n.a. PMID[24767845]
NPO10023 Francoeuria undulata Species Asteraceae Eukaryota Aerial Parts n.a. n.a. PMID[28032767]
NPO678 Streptomyces spiroverticillatus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO13302 Streptomyces nanchangensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO10023 Francoeuria undulata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO33528 Penicillium oxalicum SCSGAF 0023 Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12404 Trigonostemon chinensis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13202 Pseudodistoma kanoko Species Pseudodistomidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4866 Diospyros rotundifolia Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6632 Lunaria biennis Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO366 Pyrus communis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO366 Pyrus communis Species Rosaceae Eukaryota n.a. n.a. Database[FooDB]
NPO366 Pyrus communis Species Rosaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO366 Pyrus communis Species Rosaceae Eukaryota Pericarp n.a. n.a. Database[FooDB]
NPO366 Pyrus communis Species Rosaceae Eukaryota Fruits n.a. Database[FooDB]
NPO366 Pyrus communis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12220 Hemerocallis thunbergii Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO366 Pyrus communis Species Rosaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO366 Pyrus communis Species Rosaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO12220 Hemerocallis thunbergii Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO366 Pyrus communis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4866 Diospyros rotundifolia Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8232 Sclerocarya caffra Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13302 Streptomyces nanchangensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO8648 Gorgonia mariae Species Gorgoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14605 Glochidion thomsonii Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12404 Trigonostemon chinensis Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10620 Monochoria elata Species Pontederiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO897 Pinus gerardi Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12220 Hemerocallis thunbergii Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6632 Lunaria biennis Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13202 Pseudodistoma kanoko Species Pseudodistomidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10023 Francoeuria undulata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO678 Streptomyces spiroverticillatus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO366 Pyrus communis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11338 Muricella flexuosa Species Acanthogorgiidae 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
NPT112 Cell line MOLT-4 Homo sapiens IC50 = 5740.0 nM PMID[24767845]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 10100.0 nM PMID[24767845]

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 NPC34910 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
0.7971 Intermediate Similarity NPC284918
0.7671 Intermediate Similarity NPC264756
0.7671 Intermediate Similarity NPC477677
0.55 Remote Similarity NPC272550

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC34910 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