Natural Product: NPC123919

Natural Product IDNPC123919
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 CZZZOTXCAIDYOZ-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 5318825
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000211] Indoles and derivatives
        • [CHEMONTID:0000210] Carbazoles

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 CZZZOTXCAIDYOZ-UHFFFAOYSA-N
Standard InCHI InChI=1S/C19H19NO3/c1-10-7-13-12-8-16(22-4)15(21)9-14(12)20-17(13)11-5-6-19(2,3)23-18(10)11/h5-9,20-21H,1-4H3
SMILES Cc1cc2c3cc(c(cc3[nH]c2c2C=CC(C)(C)Oc12)O)OC

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   309.14 Volume:   321.867
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Van der Waals volume.
Dense:   0.96 LogP:   4.348
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.494
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -5.918
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The logarithm of aqueous solubility value.
Rotatable Bonds:   1.0 Rigid Bonds:   20.0
TPSA:   54.48
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Topological Polar Surface Area.
 H-Bond Acceptor:   4.0
H-Bond Donor:   2.0 Rings:   4.0
Heavy Atoms:   4.0

MedChem Properties

QED Drug-Likeness Score:   0.694 GASA:   1.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.909 Fsp3:   0.263
MCE-18:   50.0
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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:   Accepted GSK Rule:   Accepted
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   1 PAINS Alert:   0
Colloidal aggregators:   0.679 Fluc inhibitor:   0.25
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.961
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.58
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.07 Promiscuous compounds:   0.502

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.051 MDCK Permeability:   -4.778
Pgp-inhibitor:   0.129 Pgp-substrate:   0.18
PAMPA:   0.32
?
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%):   0.199 30% Bioavailability (F30%):   0.387
50% Bioavailability (F50%):   0.968

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.156 MRP1:   0.918
Plasma Protein Binding (PPB):   98.479% Volume Distribution (VD):   0.182
Fu: 1.137%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.996
OATP1B3 inhibitor:   0.996 BCRP inhibitor:   0.917
BSEP inhibitor:   0.979

ADMET: Metabolism

CYP1A2-inhibitor:   0.124 CYP1A2-substrate:   0.054
CYP2C19-inhibitor:   0.885 CYP2C19-substrate:   0.005
CYP2C9-inhibitor:   0.975 CYP2C9-substrate:   0.092
CYP2D6-inhibitor:   0.982 CYP2D6-substrate:   0.327
CYP3A4-inhibitor:   0.119 CYP3A4-substrate:   0.57
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.999
HLM stability:   0.541
?
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):  5.326 Half-life (T1/2):  1.042

ADMET: Toxicity

hERG Blockers:  0.298 hERG Blockers (10um):  0.638
Human Hepatotoxicity (H-HT):  0.67 Drug-induced Liver Injury (DILI):  0.764
AMES Toxicity:  0.792 Rat Oral Acute Toxicity:  0.712
Maximum Recommended Daily Dose:  0.796 Skin Sensitization:  0.459
Carcinogencity:  0.83 Eye Corrosion:  0.0
Eye Irritation:  0.853 Respiratory Toxicity:  0.958
Drug-induced Neurotoxicity:  0.791 Ototoxicity:  0.621
Hematotoxicity:  0.512 Drug-induced Nephrotoxicity:  0.742
Genotoxicity:  0.272 RPMI-8226 Immunitoxicity:  0.174
A549 Cytotoxicity:  0.462 Hek293 Cytotoxicity:  0.604
BCF:   1.677
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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:   4.297
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.76
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.181
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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
NPO3364 Murraya koenigii Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[12662104]
NPO3364 Murraya koenigii Species Rutaceae Eukaryota n.a. Sri Lankan n.a. PMID[23376010]
NPO3364 Murraya koenigii Species Rutaceae Eukaryota fruits Coimbatore, India 2010-JUN PMID[23691929]
NPO3364 Murraya koenigii Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[27136692]
NPO3364 Murraya koenigii Species Rutaceae Eukaryota n.a. n.a. n.a. PMID[39414752]
NPO3364 Murraya koenigii Species Rutaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3364 Murraya koenigii Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3364 Murraya koenigii Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3364 Murraya koenigii Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3364 Murraya koenigii Species Rutaceae 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 NPC123919 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
0.7167 Intermediate Similarity NPC277351
0.7119 Intermediate Similarity NPC162484
0.6949 Remote Similarity NPC99417
0.629 Remote Similarity NPC64751
0.6081 Remote Similarity NPC484123
0.6066 Remote Similarity NPC43787
0.6032 Remote Similarity NPC209769
0.5946 Remote Similarity NPC484115
0.5946 Remote Similarity NPC484114
0.5694 Remote Similarity NPC484122
0.5694 Remote Similarity NPC484119
0.5455 Remote Similarity NPC201697
0.5263 Remote Similarity NPC484124
0.5205 Remote Similarity NPC475085
0.5147 Remote Similarity NPC198503
0.5065 Remote Similarity NPC484116
0.5065 Remote Similarity NPC484117

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC123919 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