Natural Product: NPC200302

Natural Product IDNPC200302
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 STECJAGHUSJQJN-SFSMXDMGSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 11968014
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000472] Hydroxy acids and derivatives
        • [CHEMONTID:0001713] Beta hydroxy acids 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 STECJAGHUSJQJN-SFSMXDMGSA-N
Standard InCHI InChI=1S/C17H21NO4/c1-18-13-7-11(8-14(18)16-15(13)22-16)21-17(20)12(9-19)10-5-3-2-4-6-10/h2-6,11-16,19H,7-9H2,1H3/t11?,12-,13-,14+,15+,16+/m1/s1
SMILES CN1[C@@H]2CC(C[C@H]1[C@H]1[C@H]2O1)OC(=O)[C@H](CO)c1ccccc1

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   303.15 Volume:   303.974
?
Van der Waals volume.
Dense:   0.997 LogP:   0.538
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -0.03
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -1.0
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   5.0 Rigid Bonds:   18.0
TPSA:   62.3
?
Topological Polar Surface Area.
 H-Bond Acceptor:   5.0
H-Bond Donor:   1.0 Rings:   4.0
Heavy Atoms:   5.0

MedChem Properties

QED Drug-Likeness Score:   0.662 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.733 Fsp3:   0.588
MCE-18:   73.889
?
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:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.395 Fluc inhibitor:   0.001
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.02
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.163
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.016 Promiscuous compounds:   0.651

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.951 MDCK Permeability:   -4.878
Pgp-inhibitor:   0.001 Pgp-substrate:   0.185
PAMPA:   0.973
?
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):   0.019
20% Bioavailability (F20%):   0.099 30% Bioavailability (F30%):   0.956
50% Bioavailability (F50%):   0.99

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.001 MRP1:   0.35
Plasma Protein Binding (PPB):   28.349% Volume Distribution (VD):   0.417
Fu: 63.282%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.996
OATP1B3 inhibitor:   0.999 BCRP inhibitor:   0.027
BSEP inhibitor:   0.003

ADMET: Metabolism

CYP1A2-inhibitor:   0.003 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.067 CYP2C19-substrate:   0.001
CYP2C9-inhibitor:   0.852 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.001 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.228 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.001
HLM stability:   0.0
?
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):  10.882 Half-life (T1/2):  1.562

ADMET: Toxicity

hERG Blockers:  0.084 hERG Blockers (10um):  0.081
Human Hepatotoxicity (H-HT):  0.85 Drug-induced Liver Injury (DILI):  0.429
AMES Toxicity:  0.337 Rat Oral Acute Toxicity:  0.19
Maximum Recommended Daily Dose:  0.509 Skin Sensitization:  0.992
Carcinogencity:  0.021 Eye Corrosion:  0.001
Eye Irritation:  0.682 Respiratory Toxicity:  0.6
Drug-induced Neurotoxicity:  0.883 Ototoxicity:  0.718
Hematotoxicity:  0.412 Drug-induced Nephrotoxicity:  0.409
Genotoxicity:  0.609 RPMI-8226 Immunitoxicity:  0.053
A549 Cytotoxicity:  0.304 Hek293 Cytotoxicity:  0.215
BCF:   0.469
?
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:   3.024
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.242
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.598
?
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
NPO25114 Linum usitatissimum Species Linaceae Eukaryota Seeds n.a. DOI[10.1002/ejlt.201100207]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s11746-997-0093-1]
NPO6495 Datura stramonium Species Solanaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/0168-1656(92)90069-L]
NPO6495 Datura stramonium Species Solanaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jarmap.2018.11.004]
NPO24850 Datura metel Species Solanaceae Eukaryota n.a. n.a. n.a. DOI[10.3906/biy-1405-25]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota Seeds n.a. DOI[10.5219/332]
NPO18781 Hyoscyamus niger Species Solanaceae Eukaryota seeds n.a. n.a. PMID[11858758]
NPO6495 Datura stramonium Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[15374592]
NPO24850 Datura metel Species Solanaceae Eukaryota flowers Yuxi Town, Fuqing City, Fujian Province, China 2005-SEP PMID[17583953]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota n.a. n.a. n.a. PMID[22537213]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota n.a. n.a. n.a. PMID[24417583]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota Seeds n.a. n.a. PMID[26923696]
NPO6495 Datura stramonium Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[39527985]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25993 Atropa belladonna Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18781 Hyoscyamus niger Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3890 Scopolia japonica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24850 Datura metel Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6495 Datura stramonium Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10384 Scopolia carniolica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota n.a. n.a. Database[FooDB]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota Seed Oil n.a. n.a. Database[FooDB]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota n.a. n.a. Database[FooDB]
NPO10384 Scopolia carniolica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24850 Datura metel Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3890 Scopolia japonica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18781 Hyoscyamus niger Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6495 Datura stramonium Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO25993 Atropa belladonna Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6495 Datura stramonium Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18781 Hyoscyamus niger Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10384 Scopolia carniolica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO25993 Atropa belladonna Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3890 Scopolia japonica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24850 Datura metel Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6495 Datura stramonium Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18781 Hyoscyamus niger Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24850 Datura metel Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO25993 Atropa belladonna Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3890 Scopolia japonica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16326 Scopolia parviflora Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10384 Scopolia carniolica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO3890 Scopolia japonica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO25993 Atropa belladonna Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18781 Hyoscyamus niger Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO24850 Datura metel Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO6495 Datura stramonium Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18781 Hyoscyamus niger Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16326 Scopolia parviflora Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24850 Datura metel Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25114 Linum usitatissimum Species Linaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25993 Atropa belladonna Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6495 Datura stramonium Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3890 Scopolia japonica Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10384 Scopolia carniolica Species Solanaceae 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 NPC200302 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
1.0 High Similarity NPC245836
1.0 High Similarity NPC233910
1.0 High Similarity NPC39830
0.75 Intermediate Similarity NPC213126
0.75 Intermediate Similarity NPC317474
0.75 Intermediate Similarity NPC209773
0.75 Intermediate Similarity NPC609072
0.6792 Remote Similarity NPC69496
0.6792 Remote Similarity NPC161229
0.5273 Remote Similarity NPC84281
0.5273 Remote Similarity NPC169485

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC200302 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
1.0 High Similarity NPD2570 Phase 4
1.0 High Similarity NPD2571 Approved
1.0 High Similarity NPD2572 Clinical (unspecified phase)
1.0 High Similarity NPD2573 Approved
1.0 High Similarity NPD2574 Discontinued
0.9773 High Similarity NPD2566 Approved
0.75 Intermediate Similarity NPD2610 Approved
0.75 Intermediate Similarity NPD2611 Phase 4
0.75 Intermediate Similarity NPD2612 Phase 4
0.6792 Remote Similarity NPD2608 Approved
0.6792 Remote Similarity NPD2609 Approved
0.6792 Remote Similarity NPD2613 Approved
0.6731 Remote Similarity NPD2575 Phase 3
0.5263 Remote Similarity NPD3089 Approved
0.5263 Remote Similarity NPD3090 Approved
0.5179 Remote Similarity NPD3132 Phase 4
0.5172 Remote Similarity NPD3087 Approved
0.5172 Remote Similarity NPD3088 Approved
0.5085 Remote Similarity NPD3615 Approved
0.5085 Remote Similarity NPD3616 Approved

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