Natural Product: NPC486545

Natural Product IDNPC486545
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
JVEJEOJOFBJWSQ-VFGFNLGMSA-N
IUPAC Name n.a.
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 JVEJEOJOFBJWSQ-VFGFNLGMSA-N
Standard InCHI InChI=1S/C26H32O12/c1-34-18-8-12(3-5-16(18)28)7-14-15(11-36-25(14)33)24(13-4-6-17(29)19(9-13)35-2)38-26-23(32)22(31)21(30)20(10-27)37-26/h3-6,8-9,14-15,20-24,26-32H,7,10-11H2,1-2H3/t14-,15+,20+,21+,22-,23+,24-,26-/m0/s1
SMILES COc1cc(ccc1O)C[C@H]1[C@@H](COC1=O)[C@H](c1ccc(c(c1)OC)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   536.19 Volume:   511.054
?
Van der Waals volume.
Dense:   1.049 LogP:   -0.791
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -0.243
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -1.748
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The logarithm of aqueous solubility value.
Rotatable Bonds:   9.0 Rigid Bonds:   24.0
TPSA:   184.6
?
Topological Polar Surface Area.
H-Bond Acceptor:   12.0
H-Bond Donor:   6.0 Rings:   4.0
Heavy Atoms:   12.0

MedChem Properties

QED Drug-Likeness Score:   0.236 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.504 Fsp3:   0.5
MCE-18:   92.077
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
Lipinski Rule-of-5:   Accepted
Pfizer Rule:   Rejected GSK Rule:   Accepted
Golden Triangle Rule:   Accepted BMS Rule:   0
Chelating Alert:   1 PAINS Alert:   0
Colloidal aggregators:   0.562 Fluc inhibitor:   0.253
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.02
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.455
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.092 Promiscuous compounds:   0.13

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.106 MDCK Permeability:   -5.303
Pgp-inhibitor:   0.002 Pgp-substrate:   0.439
PAMPA:   0.315
?
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):   0.004
20% Bioavailability (F20%):   0.202 30% Bioavailability (F30%):   0.849
50% Bioavailability (F50%):   0.984

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.255
Plasma Protein Binding (PPB):   64.876% Volume Distribution (VD):   -0.474
Fu: 33.553%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.012
BSEP inhibitor:   0.121

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.575 CYP2C19-substrate:   0.05
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.393
CYP3A4-inhibitor:   0.525 CYP3A4-substrate:   0.217
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.081
?
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):  2.904 Half-life (T1/2):  3.42

ADMET: Toxicity

hERG Blockers:  0.033 hERG Blockers (10um):  0.24
Human Hepatotoxicity (H-HT):  0.642 Drug-induced Liver Injury (DILI):  0.612
AMES Toxicity:  0.83 Rat Oral Acute Toxicity:  0.057
Maximum Recommended Daily Dose:  0.118 Skin Sensitization:  0.998
Carcinogencity:  0.187 Eye Corrosion:  0.0
Eye Irritation:  0.071 Respiratory Toxicity:  0.062
Drug-induced Neurotoxicity:  0.107 Ototoxicity:  0.976
Hematotoxicity:  0.522 Drug-induced Nephrotoxicity:  0.934
Genotoxicity:  0.613 RPMI-8226 Immunitoxicity:  0.219
A549 Cytotoxicity:  0.493 Hek293 Cytotoxicity:  0.42
BCF:   0.506
?
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:   3.1
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.641
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   3.734
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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
NPO6409 Eutrema japonicum Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[10571166]
NPO6409 Eutrema japonicum Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[27700070]
NPO6409 Eutrema japonicum Species Brassicaceae Eukaryota Roots n.a. n.a. PMID[30232882]
NPO6409 Eutrema japonicum Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6409 Eutrema japonicum Species Brassicaceae Eukaryota n.a. n.a. Database[FooDB]
NPO6409 Eutrema japonicum Species Brassicaceae 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
NPT76 Cell line C6 Rattus norvegicus Activity = 150.7 % PMID[27700070]
NPT76 Cell line C6 Rattus norvegicus Activity = 100.4 % PMID[27700070]
NPT34 Cell line BV-2 Mus musculus IC50 > 50000.0 nM PMID[27700070]
NPT457 Cell line BT-549 Homo sapiens IC50 > 10000.0 nM PMID[27700070]
NPT81 Cell line A549 Homo sapiens IC50 > 10000.0 nM PMID[27700070]
NPT146 Cell line SK-OV-3 Homo sapiens IC50 > 10000.0 nM PMID[27700070]
NPT147 Cell line SK-MEL-2 Homo sapiens IC50 > 10000.0 nM PMID[27700070]

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 NPC486545 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
0.6575 Remote Similarity NPC278961
0.6575 Remote Similarity NPC113680
0.619 Remote Similarity NPC299706
0.619 Remote Similarity NPC115466
0.619 Remote Similarity NPC61604
0.5977 Remote Similarity NPC486549
0.5977 Remote Similarity NPC486547
0.5909 Remote Similarity NPC486546
0.5904 Remote Similarity NPC38699
0.5904 Remote Similarity NPC472711
0.5618 Remote Similarity NPC486548
0.5506 Remote Similarity NPC185307
0.5506 Remote Similarity NPC470950
0.5476 Remote Similarity NPC38041
0.5476 Remote Similarity NPC22150
0.5412 Remote Similarity NPC84181
0.5395 Remote Similarity NPC610652
0.5357 Remote Similarity NPC51328
0.5357 Remote Similarity NPC55158
0.5333 Remote Similarity NPC163635
0.5333 Remote Similarity NPC478055
0.5301 Remote Similarity NPC606627
0.5294 Remote Similarity NPC483499
0.5281 Remote Similarity NPC245615
0.5275 Remote Similarity NPC129417
0.5275 Remote Similarity NPC470235
0.5256 Remote Similarity NPC67247
0.5205 Remote Similarity NPC68779
0.5205 Remote Similarity NPC108598
0.5109 Remote Similarity NPC283995
0.5059 Remote Similarity NPC158635
0.5059 Remote Similarity NPC229882

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC486545 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