Natural Product: NPC203252

Natural Product IDNPC203252
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 UPDMQTYYPHMZOD-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 12313147
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000238] Tannins
        • [CHEMONTID:0001710] Hydrolyzable tannins

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 UPDMQTYYPHMZOD-UHFFFAOYSA-N
Standard InCHI InChI=1S/C18H14O8/c1-21-9-5-7-11-12-8(18(20)25-15(11)13(9)23-3)6-10(22-2)14(24-4)16(12)26-17(7)19/h5-6H,1-4H3
SMILES COc1cc2c3c4c(cc(c(c4oc2=O)OC)OC)c(=O)oc3c1OC

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   358.07 Volume:   334.889
?
Van der Waals volume.
Dense:   1.069 LogP:   1.978
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.187
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.034
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   21.0
TPSA:   97.34
?
Topological Polar Surface Area.
 H-Bond Acceptor:   8.0
H-Bond Donor:   0.0 Rings:   4.0
Heavy Atoms:   8.0

MedChem Properties

QED Drug-Likeness Score:   0.405 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.638 Fsp3:   0.222
MCE-18:   24.0
?
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:   0.091 Fluc inhibitor:   0.003
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.521
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.59
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.37 Promiscuous compounds:   0.41

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.596 MDCK Permeability:   -4.615
Pgp-inhibitor:   0.161 Pgp-substrate:   0.142
PAMPA:   0.136
?
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):   0.168
20% Bioavailability (F20%):   0.31 30% Bioavailability (F30%):   0.457
50% Bioavailability (F50%):   0.468

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.044 MRP1:   0.729
Plasma Protein Binding (PPB):   80.485% Volume Distribution (VD):   -0.197
Fu: 15.417%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.876
OATP1B3 inhibitor:   0.941 BCRP inhibitor:   0.023
BSEP inhibitor:   0.815

ADMET: Metabolism

CYP1A2-inhibitor:   0.425 CYP1A2-substrate:   0.837
CYP2C19-inhibitor:   0.964 CYP2C19-substrate:   0.924
CYP2C9-inhibitor:   0.075 CYP2C9-substrate:   0.001
CYP2D6-inhibitor:   0.242 CYP2D6-substrate:   0.82
CYP3A4-inhibitor:   0.967 CYP3A4-substrate:   0.344
CYP2B6-substrate:   0.002 CYP2C8-inhibitor:   0.658
HLM stability:   0.941
?
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):  6.111 Half-life (T1/2):  2.02

ADMET: Toxicity

hERG Blockers:  0.066 hERG Blockers (10um):  0.27
Human Hepatotoxicity (H-HT):  0.599 Drug-induced Liver Injury (DILI):  0.964
AMES Toxicity:  0.425 Rat Oral Acute Toxicity:  0.538
Maximum Recommended Daily Dose:  0.61 Skin Sensitization:  0.269
Carcinogencity:  0.855 Eye Corrosion:  0.11
Eye Irritation:  0.85 Respiratory Toxicity:  0.615
Drug-induced Neurotoxicity:  0.268 Ototoxicity:  0.251
Hematotoxicity:  0.546 Drug-induced Nephrotoxicity:  0.276
Genotoxicity:  0.714 RPMI-8226 Immunitoxicity:  0.176
A549 Cytotoxicity:  0.063 Hek293 Cytotoxicity:  0.326
BCF:   1.461
?
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:   3.424
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.835
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.068
?
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
NPO18280 Colubrina retusa Species n.a. n.a. n.a. n.a. n.a. PMID[10346942]
NPO18280 Colubrina retusa Species n.a. n.a. n.a. n.a. n.a. PMID[10514332]
NPO19499 Plocamium corallorhiza Species Plocamiaceae Eukaryota n.a. South African n.a. PMID[17343409]
NPO20674 Pseudopterogorgia rigida Species Gorgoniidae Eukaryota n.a. n.a. n.a. PMID[9090873]
NPO19988 Vinca herbacea Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20674 Pseudopterogorgia rigida Species Gorgoniidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22468 Parazoanthus gracilis Species Parazoanthidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18112 Melochia chamaedrys Species Malvaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13314 Callitropsis funebris Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19499 Plocamium corallorhiza Species Plocamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19988 Vinca herbacea Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13314 Callitropsis funebris Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19988 Vinca herbacea Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20615 Osmites hirsuta n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO13314 Callitropsis funebris Species Cupressaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18280 Colubrina retusa Species n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO19499 Plocamium corallorhiza Species Plocamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20550 Helenium argentinum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18639 Breynia vitis-idaea Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20674 Pseudopterogorgia rigida Species Gorgoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18112 Melochia chamaedrys Species Malvaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22468 Parazoanthus gracilis Species Parazoanthidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12448 Simplicillium lamellicola Species Cordycipitaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19988 Vinca herbacea Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20217 Vernonanthura squamulosa Species Asteraceae 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 NPC203252 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
0.7317 Intermediate Similarity NPC37502
0.7143 Intermediate Similarity NPC267627
0.6222 Remote Similarity NPC187421
0.5882 Remote Similarity NPC604162
0.5714 Remote Similarity NPC237898
0.5366 Remote Similarity NPC40702

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC203252 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