Natural Product: NPC548860

Natural Product IDNPC548860
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
5-hydroxy-6-methoxy-3-(4-methoxyphenyl)-7-[(2~{S},3~{R},4~{S},5~{R},6~{S})-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydropyran-2-yl]oxy-chromen-4-one
IUPAC Name 5-hydroxy-6-methoxy-3-(4-methoxyphenyl)-7-[(2~{S},3~{R},4~{S},5~{R},6~{S})-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydropyran-2-yl]oxy-chromen-4-one
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]

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 XKNZYDKRYPYTHS-BHPXHZLCSA-N
Standard InCHI InChI=1S/C23H24O11/c1-30-11-5-3-10(4-6-11)12-9-32-13-7-14(22(31-2)19(27)16(13)17(12)25)33-23-21(29)20(28)18(26)15(8-24)34-23/h3-7,9,15,18,20-21,23-24,26-29H,8H2,1-2H3/t15-,18-,20-,21+,23+/m0/s1
SMILES COC1=CC=C(C2=COC3=CC(O[C@@H]4O[C@@H](CO)[C@H](O)[C@H](O)[C@H]4O)=C(OC)C(O)=C3C2=O)C=C1

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   476.13 Volume:   447.739
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Van der Waals volume.
Dense:   1.063 LogP:   1.144
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.768
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.061
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The logarithm of aqueous solubility value.
Rotatable Bonds:   6.0 Rigid Bonds:   24.0
TPSA:   168.28
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Topological Polar Surface Area.
H-Bond Acceptor:   11.0
H-Bond Donor:   5.0 Rings:   4.0
Heavy Atoms:   11.0

MedChem Properties

QED Drug-Likeness Score:   0.333 GASA:   0.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.877 Fsp3:   0.348
MCE-18:   86.387
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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:   1 PAINS Alert:   0
Colloidal aggregators:   0.494 Fluc inhibitor:   0.382
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.79
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.683
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.084 Promiscuous compounds:   0.233

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.249 MDCK Permeability:   -5.422
Pgp-inhibitor:   0.002 Pgp-substrate:   0.305
PAMPA:   0.969
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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):   0.985
20% Bioavailability (F20%):   0.634 30% Bioavailability (F30%):   0.972
50% Bioavailability (F50%):   0.992

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.022 MRP1:   0.408
Plasma Protein Binding (PPB):   91.17% Volume Distribution (VD):   -0.272
Fu: 7.581%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   0.989
OATP1B3 inhibitor:   0.998 BCRP inhibitor:   0.467
BSEP inhibitor:   0.01

ADMET: Metabolism

CYP1A2-inhibitor:   0.326 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.492 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.259
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.99
HLM stability:   0.003
?
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):  2.44 Half-life (T1/2):  1.754

ADMET: Toxicity

hERG Blockers:  0.034 hERG Blockers (10um):  0.218
Human Hepatotoxicity (H-HT):  0.708 Drug-induced Liver Injury (DILI):  0.974
AMES Toxicity:  0.898 Rat Oral Acute Toxicity:  0.123
Maximum Recommended Daily Dose:  0.085 Skin Sensitization:  0.981
Carcinogencity:  0.392 Eye Corrosion:  0.0
Eye Irritation:  0.359 Respiratory Toxicity:  0.102
Drug-induced Neurotoxicity:  0.084 Ototoxicity:  0.774
Hematotoxicity:  0.462 Drug-induced Nephrotoxicity:  0.795
Genotoxicity:  0.793 RPMI-8226 Immunitoxicity:  0.2
A549 Cytotoxicity:  0.473 Hek293 Cytotoxicity:  0.277
BCF:   0.374
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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:   3.183
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.717
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   3.862
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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
NPO2865 Abrus precatorius Species Fabaceae Eukaryota aerial parts n.a. n.a. PMID[19299148]
NPO2865 Abrus precatorius Species Fabaceae Eukaryota n.a. leaf n.a. PMID[22210168]
NPO2865 Abrus precatorius Species Fabaceae Eukaryota n.a. stem n.a. PMID[22210168]
NPO2865 Abrus precatorius Species Fabaceae Eukaryota Leaves n.a. n.a. PMID[2691636]
NPO2865 Abrus precatorius Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[2691636]
NPO2865 Abrus precatorius Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2865 Abrus precatorius Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2865 Abrus precatorius Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2865 Abrus precatorius Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2865 Abrus precatorius Species Fabaceae 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 NPC548860 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
0.8611 High Similarity NPC205076
0.8514 High Similarity NPC307518
0.8 Intermediate Similarity NPC224462
0.7973 Intermediate Similarity NPC73511
0.7922 Intermediate Similarity NPC48773
0.7568 Intermediate Similarity NPC135345
0.7333 Intermediate Similarity NPC45165
0.7143 Intermediate Similarity NPC156457
0.6835 Remote Similarity NPC186807
0.6709 Remote Similarity NPC197896
0.6709 Remote Similarity NPC105511
0.6709 Remote Similarity NPC258035
0.6709 Remote Similarity NPC313163
0.6585 Remote Similarity NPC229729
0.65 Remote Similarity NPC161749
0.65 Remote Similarity NPC234739
0.65 Remote Similarity NPC603782
0.6463 Remote Similarity NPC481043
0.6456 Remote Similarity NPC160515
0.6375 Remote Similarity NPC58053
0.6341 Remote Similarity NPC100720
0.6071 Remote Similarity NPC479402
0.6 Remote Similarity NPC21666
0.6 Remote Similarity NPC601607
0.5952 Remote Similarity NPC138540
0.5909 Remote Similarity NPC487212
0.5882 Remote Similarity NPC479401
0.5882 Remote Similarity NPC80140
0.5882 Remote Similarity NPC609451
0.5875 Remote Similarity NPC25547
0.5862 Remote Similarity NPC479407
0.5833 Remote Similarity NPC105025
0.5806 Remote Similarity NPC257714
0.5765 Remote Similarity NPC117260
0.5765 Remote Similarity NPC201292
0.5714 Remote Similarity NPC479405
0.5698 Remote Similarity NPC488071
0.5652 Remote Similarity NPC479404
0.5647 Remote Similarity NPC603655
0.5632 Remote Similarity NPC605067
0.5616 Remote Similarity NPC216769
0.5595 Remote Similarity NPC259070
0.5595 Remote Similarity NPC348541
0.5568 Remote Similarity NPC479406
0.5568 Remote Similarity NPC602805
0.5529 Remote Similarity NPC95090
0.5529 Remote Similarity NPC27408
0.5506 Remote Similarity NPC488072
0.5465 Remote Similarity NPC24043
0.5412 Remote Similarity NPC211014
0.5393 Remote Similarity NPC607201
0.5376 Remote Similarity NPC475155
0.5349 Remote Similarity NPC93337
0.5349 Remote Similarity NPC487213
0.5287 Remote Similarity NPC45638
0.5275 Remote Similarity NPC211594
0.527 Remote Similarity NPC116632
0.527 Remote Similarity NPC35763
0.5233 Remote Similarity NPC289667
0.5227 Remote Similarity NPC472459
0.5222 Remote Similarity NPC607707
0.5111 Remote Similarity NPC243930
0.5057 Remote Similarity NPC143851
0.5052 Remote Similarity NPC479403

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC548860 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
0.65 Remote Similarity NPD4381 Clinical (unspecified phase)

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