Natural Product: NPC17308

Natural Product IDNPC17308
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 XMOCLSLCDHWDHP-WPZCJLIBSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 12309543
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0000337] Flavans
          • [CHEMONTID:0003012] Flavan-3-ols
            • [CHEMONTID:0001584] Catechins
              • [CHEMONTID:0001594] Epigallocatechins

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 XMOCLSLCDHWDHP-WPZCJLIBSA-N
Standard InCHI InChI=1S/C15H14O7/c16-7-3-9(17)8-5-12(20)15(22-13(8)4-7)6-1-10(18)14(21)11(19)2-6/h1-4,12,15-21H,5H2/t12?,15-/m1/s1
SMILES c1c(cc(c(c1O)O)O)[C@@H]1C(Cc2c(cc(cc2O1)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   306.07 Volume:   288.04
?
Van der Waals volume.
Dense:   1.063 LogP:   0.711
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.233
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.469
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   1.0 Rigid Bonds:   17.0
TPSA:   130.61
?
Topological Polar Surface Area.
 H-Bond Acceptor:   7.0
H-Bond Donor:   6.0 Rings:   3.0
Heavy Atoms:   7.0

MedChem Properties

QED Drug-Likeness Score:   0.437 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.521 Fsp3:   0.2
MCE-18:   63.333
?
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:   1 PAINS Alert:   1
Colloidal aggregators:   0.721 Fluc inhibitor:   0.361
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.188
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.083
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.522 Promiscuous compounds:   0.528

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.461 MDCK Permeability:   -4.973
Pgp-inhibitor:   0.0 Pgp-substrate:   0.04
PAMPA:   0.756
?
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):   0.043
20% Bioavailability (F20%):   0.982 30% Bioavailability (F30%):   0.996
50% Bioavailability (F50%):   0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.037 MRP1:   0.882
Plasma Protein Binding (PPB):   88.653% Volume Distribution (VD):   0.055
Fu: 19.878%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.963
OATP1B3 inhibitor:   0.985 BCRP inhibitor:   0.284
BSEP inhibitor:   0.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.131 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.001
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.001
CYP3A4-inhibitor:   0.008 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.839
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):  11.298 Half-life (T1/2):  2.161

ADMET: Toxicity

hERG Blockers:  0.147 hERG Blockers (10um):  0.83
Human Hepatotoxicity (H-HT):  0.548 Drug-induced Liver Injury (DILI):  0.34
AMES Toxicity:  0.505 Rat Oral Acute Toxicity:  0.396
Maximum Recommended Daily Dose:  0.891 Skin Sensitization:  0.996
Carcinogencity:  0.178 Eye Corrosion:  0.005
Eye Irritation:  0.979 Respiratory Toxicity:  0.649
Drug-induced Neurotoxicity:  0.007 Ototoxicity:  0.902
Hematotoxicity:  0.015 Drug-induced Nephrotoxicity:  0.012
Genotoxicity:  0.984 RPMI-8226 Immunitoxicity:  0.007
A549 Cytotoxicity:  0.96 Hek293 Cytotoxicity:  0.628
BCF:   0.54
?
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:   3.002
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.124
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.435
?
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
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota Seeds Anhui province, China DOI[10.1016/j.foodres.2020.109416]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota Seeds Gansu province, China DOI[10.1016/j.foodres.2020.109416]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota Seeds Henan province, China DOI[10.1016/j.foodres.2020.109416]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota Seeds Shandong province, China DOI[10.1016/j.foodres.2020.109416]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota Seeds Shanxi province, China DOI[10.1016/j.foodres.2020.109416]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota n.a. root n.a. DOI[10.2174/092986712800229032]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota n.a. n.a. n.a. PMID[19402674]
NPO30226 Paeonia albiflora Species Paeoniaceae Eukaryota roots n.a. n.a. PMID[19691309]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota n.a. root n.a. PMID[19721258]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota n.a. root n.a. PMID[19772486]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota Roots n.a. n.a. PMID[20806783]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota n.a. root n.a. PMID[21782011]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota n.a. root n.a. PMID[22190295]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota n.a. seed n.a. PMID[23497864]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota n.a. root n.a. PMID[26838074]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota n.a. root n.a. PMID[27313650]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota n.a. root n.a. PMID[27429639]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota Roots n.a. n.a. PMID[29741372]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota Seeds HeZe, ShanDong, China early autumn (from August to the beginning of September PMID[32545196]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota Roots n.a. n.a. PMID[32951423]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota Seeds Xinjiang,China PMID[33063333]
NPO21458 Radix paeoniae rubra Species Lymnaeidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2340 Caulis spatholobi n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO277 Caulis millettiae n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO30226 Paeonia albiflora Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28024 Rheum palmatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20881 Rheum officinale Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7632 Rheum tanguticum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2340 Caulis spatholobi n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO7632 Rheum tanguticum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28024 Rheum palmatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30226 Paeonia albiflora Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20881 Rheum officinale Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28024 Rheum palmatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7632 Rheum tanguticum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21458 Radix paeoniae rubra Species Lymnaeidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO277 Caulis millettiae n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20881 Rheum officinale Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2340 Caulis spatholobi n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO20881 Rheum officinale Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7632 Rheum tanguticum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28024 Rheum palmatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30226 Paeonia albiflora Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7632 Rheum tanguticum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20881 Rheum officinale Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28024 Rheum palmatum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7632 Rheum tanguticum Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20881 Rheum officinale Species Polygonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9798 Paeonia lactiflora Species Paeoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28024 Rheum palmatum Species Polygonaceae 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 NPC17308 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 NPC268266
1.0 High Similarity NPC42760
1.0 High Similarity NPC220825
1.0 High Similarity NPC268342
0.7826 Intermediate Similarity NPC261619
0.7826 Intermediate Similarity NPC61477
0.7826 Intermediate Similarity NPC78770
0.7826 Intermediate Similarity NPC219876
0.7826 Intermediate Similarity NPC126029
0.7826 Intermediate Similarity NPC15658
0.7447 Intermediate Similarity NPC47398
0.7447 Intermediate Similarity NPC234333
0.7447 Intermediate Similarity NPC260898
0.7391 Intermediate Similarity NPC207179
0.7391 Intermediate Similarity NPC167571
0.7391 Intermediate Similarity NPC278552
0.6909 Remote Similarity NPC96576
0.6667 Remote Similarity NPC9636
0.6667 Remote Similarity NPC61946
0.6415 Remote Similarity NPC16435
0.6415 Remote Similarity NPC171932
0.6333 Remote Similarity NPC308402
0.6275 Remote Similarity NPC19721
0.6102 Remote Similarity NPC607430
0.5806 Remote Similarity NPC28440
0.5625 Remote Similarity NPC470802
0.5574 Remote Similarity NPC58190
0.5574 Remote Similarity NPC108811
0.5574 Remote Similarity NPC170103
0.5574 Remote Similarity NPC236202
0.5574 Remote Similarity NPC262911
0.5574 Remote Similarity NPC202742
0.5538 Remote Similarity NPC601997
0.5538 Remote Similarity NPC609211
0.5538 Remote Similarity NPC610665
0.5536 Remote Similarity NPC291948
0.5536 Remote Similarity NPC104983
0.5536 Remote Similarity NPC250436
0.5536 Remote Similarity NPC300845
0.5536 Remote Similarity NPC88803
0.5484 Remote Similarity NPC246202
0.5484 Remote Similarity NPC224161
0.5484 Remote Similarity NPC46335
0.5484 Remote Similarity NPC294558
0.5484 Remote Similarity NPC18185
0.5484 Remote Similarity NPC263940
0.5484 Remote Similarity NPC279406
0.5484 Remote Similarity NPC486519
0.5455 Remote Similarity NPC600630
0.5455 Remote Similarity NPC607896
0.5455 Remote Similarity NPC611369
0.527 Remote Similarity NPC600812
0.5192 Remote Similarity NPC482472
0.5192 Remote Similarity NPC601844
0.5161 Remote Similarity NPC289990
0.5161 Remote Similarity NPC605048
0.5147 Remote Similarity NPC65333
0.5147 Remote Similarity NPC278548
0.5091 Remote Similarity NPC325028
0.5091 Remote Similarity NPC256346
0.5091 Remote Similarity NPC606550
0.5082 Remote Similarity NPC38779
0.5082 Remote Similarity NPC114179
0.5082 Remote Similarity NPC68324
0.5082 Remote Similarity NPC289322
0.5082 Remote Similarity NPC156818
0.5082 Remote Similarity NPC160512
0.5079 Remote Similarity NPC277331
0.5079 Remote Similarity NPC100482
0.5075 Remote Similarity NPC226809
0.5072 Remote Similarity NPC44192
0.507 Remote Similarity NPC135021

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC17308 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
0.7826 Intermediate Similarity NPD1612 Clinical (unspecified phase)
0.7826 Intermediate Similarity NPD1613 Phase 4
0.5536 Remote Similarity NPD4868 Phase 3
0.5132 Remote Similarity NPD7993 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