Natural Product: NPC475147

Natural Product IDNPC475147
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 10-O-Methyljerantinine A
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL499341
PubChem CID 25112287
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000279] Alkaloids and derivatives
      • [CHEMONTID:0002672] Plumeran-type alkaloids

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 KYSSJRZIVJUXLG-VABKMULXSA-N
Standard InCHI InChI=1S/C23H28N2O4/c1-5-22-7-6-9-25-10-8-23(21(22)25)15-11-17(27-2)18(28-3)12-16(15)24-19(23)14(13-22)20(26)29-4/h6-7,11-12,21,24H,5,8-10,13H2,1-4H3/t21-,22-,23-/m0/s1
SMILES CCC12CC(=C3C4(C1N(CC4)CC=C2)C5=CC(=C(C=C5N3)OC)OC)C(=O)OC

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   396.2 Volume:   404.917
?
Van der Waals volume.
Dense:   0.978 LogP:   3.168
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.017
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.027
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   5.0 Rigid Bonds:   24.0
TPSA:   60.03
?
Topological Polar Surface Area.
 H-Bond Acceptor:   6.0
H-Bond Donor:   1.0 Rings:   5.0
Heavy Atoms:   6.0

MedChem Properties

QED Drug-Likeness Score:   0.623 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.606 Fsp3:   0.522
MCE-18:   132.0
?
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:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.066 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.64
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.603
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.001 Promiscuous compounds:   0.068

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.76 MDCK Permeability:   -4.824
Pgp-inhibitor:   0.179 Pgp-substrate:   0.98
PAMPA:   0.006
?
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):   0.058
20% Bioavailability (F20%):   0.205 30% Bioavailability (F30%):   0.642
50% Bioavailability (F50%):   0.936

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.345 MRP1:   0.994
Plasma Protein Binding (PPB):   85.886% Volume Distribution (VD):   0.734
Fu: 10.987%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.717
OATP1B3 inhibitor:   0.909 BCRP inhibitor:   0.665
BSEP inhibitor:   0.985

ADMET: Metabolism

CYP1A2-inhibitor:   0.985 CYP1A2-substrate:   0.057
CYP2C19-inhibitor:   0.992 CYP2C19-substrate:   0.012
CYP2C9-inhibitor:   0.013 CYP2C9-substrate:   0.008
CYP2D6-inhibitor:   0.985 CYP2D6-substrate:   0.612
CYP3A4-inhibitor:   0.997 CYP3A4-substrate:   0.208
CYP2B6-substrate:   0.241 CYP2C8-inhibitor:   0.45
HLM stability:   0.458
?
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):  9.656 Half-life (T1/2):  1.7

ADMET: Toxicity

hERG Blockers:  0.141 hERG Blockers (10um):  0.428
Human Hepatotoxicity (H-HT):  0.61 Drug-induced Liver Injury (DILI):  0.39
AMES Toxicity:  0.294 Rat Oral Acute Toxicity:  0.455
Maximum Recommended Daily Dose:  0.848 Skin Sensitization:  0.137
Carcinogencity:  0.431 Eye Corrosion:  0.0
Eye Irritation:  0.041 Respiratory Toxicity:  0.775
Drug-induced Neurotoxicity:  0.56 Ototoxicity:  0.718
Hematotoxicity:  0.367 Drug-induced Nephrotoxicity:  0.516
Genotoxicity:  0.827 RPMI-8226 Immunitoxicity:  0.045
A549 Cytotoxicity:  0.061 Hek293 Cytotoxicity:  0.412
BCF:   0.996
?
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:   3.811
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.285
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.667
?
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
NPO9376 Tabernaemontana corymbosa Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[18778099]
NPO9376 Tabernaemontana corymbosa Species Apocynaceae Eukaryota n.a. leaf n.a. PMID[18778099]
NPO9376 Tabernaemontana corymbosa Species Apocynaceae Eukaryota Leaves n.a. n.a. PMID[24773071]
NPO9376 Tabernaemontana corymbosa Species Apocynaceae Eukaryota stem-bark Pahang, Malaysia 2003-JUN PMID[25919190]
NPO9376 Tabernaemontana corymbosa Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[26918761]
NPO9376 Tabernaemontana corymbosa Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[27077800]
NPO9376 Tabernaemontana corymbosa Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[29319316]
NPO9376 Tabernaemontana corymbosa Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[30869890]
NPO9376 Tabernaemontana corymbosa Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[32356659]
NPO9376 Tabernaemontana corymbosa Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9376 Tabernaemontana corymbosa Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9376 Tabernaemontana corymbosa Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]

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
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 12000.0 nM PMID[18778099]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 13600.0 nM PMID[18778099]

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 NPC475147 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
0.9275 High Similarity NPC475133
0.8194 Intermediate Similarity NPC22476
0.7867 Intermediate Similarity NPC119722
0.7432 Intermediate Similarity NPC123241
0.7143 Intermediate Similarity NPC203628
0.7051 Intermediate Similarity NPC303214
0.7051 Intermediate Similarity NPC5630
0.6875 Remote Similarity NPC232600
0.6835 Remote Similarity NPC195636
0.6543 Remote Similarity NPC87714
0.6386 Remote Similarity NPC476069
0.5789 Remote Similarity NPC77812
0.5789 Remote Similarity NPC303387
0.5765 Remote Similarity NPC186669
0.5765 Remote Similarity NPC269449
0.5743 Remote Similarity NPC469722
0.5619 Remote Similarity NPC485928
0.5619 Remote Similarity NPC477068
0.5506 Remote Similarity NPC19175
0.5455 Remote Similarity NPC189661
0.5392 Remote Similarity NPC483959
0.5315 Remote Similarity NPC111877
0.5287 Remote Similarity NPC293458
0.5221 Remote Similarity NPC115588
0.5169 Remote Similarity NPC485981
0.513 Remote Similarity NPC485929
0.5119 Remote Similarity NPC61013
0.5054 Remote Similarity NPC128476

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC475147 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