Natural Product: NPC483423

Natural Product IDNPC483423
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 VFFGPZNMSGJRRP-MRVPVSSYSA-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]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0001890] Isocoumarins and derivatives

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 VFFGPZNMSGJRRP-MRVPVSSYSA-N
Standard InCHI InChI=1S/C13H13ClO5/c1-18-9-2-7-3-10(4-8(15)6-14)19-13(17)12(7)11(16)5-9/h2-3,5,8,15-16H,4,6H2,1H3/t8-/m1/s1
SMILES COc1cc2cc(C[C@H](CCl)O)oc(=O)c2c(c1)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   284.05 Volume:   262.271
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Van der Waals volume.
Dense:   1.083 LogP:   2.249
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.064
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.62
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The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   12.0
TPSA:   79.9
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Topological Polar Surface Area.
 H-Bond Acceptor:   5.0
H-Bond Donor:   2.0 Rings:   2.0
Heavy Atoms:   6.0

MedChem Properties

QED Drug-Likeness Score:   0.835 GASA:   0.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.222 Fsp3:   0.308
MCE-18:   26.0
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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:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   1
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.717 Fluc inhibitor:   0.218
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.606
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.389
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.984 Promiscuous compounds:   0.357

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.178 MDCK Permeability:   -4.832
Pgp-inhibitor:   0.0 Pgp-substrate:   0.013
PAMPA:   0.975
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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):   0.002
20% Bioavailability (F20%):   0.615 30% Bioavailability (F30%):   0.928
50% Bioavailability (F50%):   0.985

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.001 MRP1:   0.2
Plasma Protein Binding (PPB):   53.779% Volume Distribution (VD):   0.198
Fu: 43.293%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.956
OATP1B3 inhibitor:   0.878 BCRP inhibitor:   0.01
BSEP inhibitor:   0.804

ADMET: Metabolism

CYP1A2-inhibitor:   0.976 CYP1A2-substrate:   0.503
CYP2C19-inhibitor:   0.043 CYP2C19-substrate:   0.021
CYP2C9-inhibitor:   0.364 CYP2C9-substrate:   0.923
CYP2D6-inhibitor:   0.762 CYP2D6-substrate:   0.846
CYP3A4-inhibitor:   0.001 CYP3A4-substrate:   0.013
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.383
HLM stability:   0.871
?
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):  5.378 Half-life (T1/2):  1.289

ADMET: Toxicity

hERG Blockers:  0.084 hERG Blockers (10um):  0.34
Human Hepatotoxicity (H-HT):  0.595 Drug-induced Liver Injury (DILI):  0.646
AMES Toxicity:  0.876 Rat Oral Acute Toxicity:  0.438
Maximum Recommended Daily Dose:  0.768 Skin Sensitization:  0.838
Carcinogencity:  0.716 Eye Corrosion:  0.753
Eye Irritation:  0.967 Respiratory Toxicity:  0.955
Drug-induced Neurotoxicity:  0.393 Ototoxicity:  0.702
Hematotoxicity:  0.45 Drug-induced Nephrotoxicity:  0.548
Genotoxicity:  0.865 RPMI-8226 Immunitoxicity:  0.135
A549 Cytotoxicity:  0.357 Hek293 Cytotoxicity:  0.357
BCF:   0.617
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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:   3.294
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.584
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.956
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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
NPO14254 Kandelia candel Species Rhizophoraceae Eukaryota n.a. n.a. n.a. PMID[17944538]
NPO14254 Kandelia candel Species Rhizophoraceae Eukaryota n.a. n.a. n.a. PMID[22823026]
NPO14254 Kandelia candel Species Rhizophoraceae Eukaryota leaves and stems Ha Long, Quang Ninh province, Vietnam 2014-Jul PMID[25769817]
NPO14254 Kandelia candel Species Rhizophoraceae Eukaryota n.a. n.a. n.a. PMID[29792702]
NPO14254 Kandelia candel Species Rhizophoraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14254 Kandelia candel Species Rhizophoraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14254 Kandelia candel Species Rhizophoraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14254 Kandelia candel Species Rhizophoraceae 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
NPT2 Others Unspecified n.a. Inhibition = 41.0 % PMID[29792702]

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 NPC483423 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
0.8077 Intermediate Similarity NPC283229
0.8 Intermediate Similarity NPC140641
0.8 Intermediate Similarity NPC481538
0.7692 Intermediate Similarity NPC71735
0.7222 Intermediate Similarity NPC483424
0.7143 Intermediate Similarity NPC483429
0.5902 Remote Similarity NPC483422
0.541 Remote Similarity NPC483428
0.5167 Remote Similarity NPC356353
0.5082 Remote Similarity NPC483427
0.5079 Remote Similarity NPC483421
0.5079 Remote Similarity NPC483420

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC483423 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
0.5246 Remote Similarity NPD970 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