Natural Product: NPC483842

Natural Product IDNPC483842
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
QTNJSHMGSSFWDT-UZOCENSHSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 134133937
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 QTNJSHMGSSFWDT-UZOCENSHSA-N
Standard InCHI InChI=1S/C28H34O10/c1-15-12-13-20(35-17(3)30)27(14-34-16(2)29)24(37-25(33)19-10-8-7-9-11-19)22(32)21-23(36-18(4)31)28(15,27)38-26(21,5)6/h7-11,15,20-21,23-24H,12-14H2,1-6H3/t15-,20+,21-,23-,24-,27+,28-/m1/s1
SMILES C[C@@H]1CC[C@@H]([C@@]2(COC(=O)C)[C@@H](C(=O)[C@@H]3[C@H]([C@]12OC3(C)C)OC(=O)C)OC(=O)c1ccccc1)OC(=O)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   530.22 Volume:   525.429
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Van der Waals volume.
Dense:   1.009 LogP:   2.173
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.408
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.753
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The logarithm of aqueous solubility value.
Rotatable Bonds:   10.0 Rigid Bonds:   25.0
TPSA:   131.5
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Topological Polar Surface Area.
H-Bond Acceptor:   10.0
H-Bond Donor:   0.0 Rings:   4.0
Heavy Atoms:   10.0

MedChem Properties

QED Drug-Likeness Score:   0.399 GASA:   1.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   5.713 Fsp3:   0.607
MCE-18:   142.222
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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:   Accepted BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.249 Fluc inhibitor:   0.014
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.008
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.101
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.215 Promiscuous compounds:   0.104

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.028 MDCK Permeability:   -4.651
Pgp-inhibitor:   0.999 Pgp-substrate:   0.127
PAMPA:   0.359
?
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%):   0.03 30% Bioavailability (F30%):   0.622
50% Bioavailability (F50%):   0.915

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.017 MRP1:   0.997
Plasma Protein Binding (PPB):   71.717% Volume Distribution (VD):   -0.447
Fu: 27.489%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   0.998 BCRP inhibitor:   0.307
BSEP inhibitor:   0.986

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.096
CYP2C19-inhibitor:   0.001 CYP2C19-substrate:   0.007
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.497
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.017
CYP3A4-inhibitor:   0.004 CYP3A4-substrate:   0.034
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.958
?
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):  5.154 Half-life (T1/2):  0.434

ADMET: Toxicity

hERG Blockers:  0.033 hERG Blockers (10um):  0.389
Human Hepatotoxicity (H-HT):  0.16 Drug-induced Liver Injury (DILI):  0.884
AMES Toxicity:  0.581 Rat Oral Acute Toxicity:  0.228
Maximum Recommended Daily Dose:  0.17 Skin Sensitization:  0.957
Carcinogencity:  0.678 Eye Corrosion:  0.001
Eye Irritation:  0.405 Respiratory Toxicity:  0.019
Drug-induced Neurotoxicity:  0.131 Ototoxicity:  0.201
Hematotoxicity:  0.105 Drug-induced Nephrotoxicity:  0.396
Genotoxicity:  0.875 RPMI-8226 Immunitoxicity:  0.067
A549 Cytotoxicity:  0.054 Hek293 Cytotoxicity:  0.179
BCF:   0.775
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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:   3.762
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.595
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   5.082
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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
NPO40494 Maytenus bilocularis Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[27120798]

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
NPT27556 Single protein L-type amino acid transporter 3 Homo sapiens IC50 = 151200.0 nM PMID[27120798]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. FC = 1.9 n.a. PMID[27120798]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Inhibition > 30.0 % PMID[27120798]
NPT2 Others Unspecified n.a. FC = 50.6 n.a. PMID[27120798]

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 NPC483842 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
0.7246 Intermediate Similarity NPC254558
0.7246 Intermediate Similarity NPC471100
0.7246 Intermediate Similarity NPC605884
0.7206 Intermediate Similarity NPC90257
0.7206 Intermediate Similarity NPC483845
0.7206 Intermediate Similarity NPC69357
0.7059 Intermediate Similarity NPC17877
0.6901 Remote Similarity NPC306146
0.6901 Remote Similarity NPC483841
0.6901 Remote Similarity NPC483844
0.6761 Remote Similarity NPC471107
0.6622 Remote Similarity NPC483848
0.6533 Remote Similarity NPC483849
0.625 Remote Similarity NPC48017
0.6216 Remote Similarity NPC471103
0.6027 Remote Similarity NPC246480
0.5974 Remote Similarity NPC282239
0.5974 Remote Similarity NPC471102
0.5694 Remote Similarity NPC211137
0.5694 Remote Similarity NPC66761
0.5694 Remote Similarity NPC483843
0.5634 Remote Similarity NPC474608
0.557 Remote Similarity NPC51602
0.5541 Remote Similarity NPC483847
0.5526 Remote Similarity NPC483846
0.5526 Remote Similarity NPC137718
0.5526 Remote Similarity NPC148062
0.5513 Remote Similarity NPC252314
0.5479 Remote Similarity NPC475429
0.5479 Remote Similarity NPC476094
0.5476 Remote Similarity NPC473115
0.5467 Remote Similarity NPC473060
0.5467 Remote Similarity NPC51314
0.5455 Remote Similarity NPC171207
0.5417 Remote Similarity NPC283375
0.5417 Remote Similarity NPC183122
0.5395 Remote Similarity NPC4341
0.5395 Remote Similarity NPC479047
0.5395 Remote Similarity NPC291638
0.5395 Remote Similarity NPC147880
0.5385 Remote Similarity NPC41481
0.5333 Remote Similarity NPC475759
0.5333 Remote Similarity NPC470152
0.5316 Remote Similarity NPC479043
0.5256 Remote Similarity NPC473758
0.5195 Remote Similarity NPC191082
0.519 Remote Similarity NPC479044
0.5125 Remote Similarity NPC57628
0.5125 Remote Similarity NPC481059
0.5119 Remote Similarity NPC479040

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC483842 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