Natural Product: NPC166885

Natural Product IDNPC166885
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 UZOHDKGTYVTYDZ-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 160483
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0000018] Anthracenes
        • [CHEMONTID:0001911] Anthracenecarboxylic acids and derivatives
          • [CHEMONTID:0002424] Anthracenecarboxylic acids

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 UZOHDKGTYVTYDZ-UHFFFAOYSA-N
Standard InCHI InChI=1S/C16H10O7/c1-5-2-7-12(14(20)10(5)16(22)23)15(21)11-8(13(7)19)3-6(17)4-9(11)18/h2-4,17-18,20H,1H3,(H,22,23)
SMILES Cc1cc2c(c(c1C(=O)O)O)C(=O)c1c(cc(cc1O)O)C2=O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   314.04 Volume:   297.426
?
Van der Waals volume.
Dense:   1.056 LogP:   2.998
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.298
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -5.208
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   1.0 Rigid Bonds:   19.0
TPSA:   132.13
?
Topological Polar Surface Area.
 H-Bond Acceptor:   7.0
H-Bond Donor:   4.0 Rings:   3.0
Heavy Atoms:   7.0

MedChem Properties

QED Drug-Likeness Score:   0.536 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.576 Fsp3:   0.062
MCE-18:   42.0
?
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:   0
Chelating Alert:   1 PAINS Alert:   1
Colloidal aggregators:   0.169 Fluc inhibitor:   0.331
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.103
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.376
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.551 Promiscuous compounds:   0.55

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.565 MDCK Permeability:   -4.843
Pgp-inhibitor:   0.005 Pgp-substrate:   0.015
PAMPA:   0.997
?
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):   0.067
20% Bioavailability (F20%):   0.008 30% Bioavailability (F30%):   0.214
50% Bioavailability (F50%):   0.749

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.977
Plasma Protein Binding (PPB):   97.823% Volume Distribution (VD):   -0.782
Fu: 1.207%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.755
OATP1B3 inhibitor:   0.992 BCRP inhibitor:   0.016
BSEP inhibitor:   0.006

ADMET: Metabolism

CYP1A2-inhibitor:   0.65 CYP1A2-substrate:   0.02
CYP2C19-inhibitor:   0.027 CYP2C19-substrate:   0.052
CYP2C9-inhibitor:   0.097 CYP2C9-substrate:   0.16
CYP2D6-inhibitor:   0.002 CYP2D6-substrate:   0.065
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.012
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.999
HLM stability:   0.563
?
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):  0.387 Half-life (T1/2):  1.623

ADMET: Toxicity

hERG Blockers:  0.022 hERG Blockers (10um):  0.142
Human Hepatotoxicity (H-HT):  0.65 Drug-induced Liver Injury (DILI):  0.969
AMES Toxicity:  0.838 Rat Oral Acute Toxicity:  0.432
Maximum Recommended Daily Dose:  0.373 Skin Sensitization:  0.843
Carcinogencity:  0.579 Eye Corrosion:  0.0
Eye Irritation:  0.99 Respiratory Toxicity:  0.885
Drug-induced Neurotoxicity:  0.105 Ototoxicity:  0.553
Hematotoxicity:  0.686 Drug-induced Nephrotoxicity:  0.778
Genotoxicity:  0.981 RPMI-8226 Immunitoxicity:  0.172
A549 Cytotoxicity:  0.738 Hek293 Cytotoxicity:  0.298
BCF:   0.635
?
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:   3.099
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.251
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.714
?
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
NPO64812 Astragalus lebbeck + Pestalotiopsis acaciae symbiont Species n.a. n.a. n.a. n.a. n.a. DOI[10.1016/j.tetlet.2013.08.054]
NPO15822 Stypopodium zonale Species Dictyotaceae Eukaryota n.a. n.a. n.a. PMID[10395524]
NPO15822 Stypopodium zonale Species Dictyotaceae Eukaryota n.a. n.a. n.a. PMID[12444716]
NPO28888 Magnaporthe grisea Species Magnaporthaceae Eukaryota n.a. n.a. n.a. PMID[16869509]
NPO18853 Alstonia scholaris Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[21043460]
NPO24093 Drynaria fortunei Species Polypodiaceae Eukaryota n.a. n.a. n.a. PMID[21377852]
NPO41895 A new engineered strain of Saccharomyces cerevisiae INVSc1 [bAS, CPR, CYP72A63, CYP93E2 or CYP716A12] Strain Saccharomycetaceae Eukaryota n.a. n.a. n.a. PMID[23378447]
NPO22674 Caulerpa racemosa Species Caulerpaceae Eukaryota n.a. n.a. n.a. PMID[23548547]
NPO24324 Halobacterium salinarum Species Halobacteriaceae Archaea n.a. n.a. n.a. PMID[24823651]
NPO7118 Manglietiastrum sinicum Species Magnoliaceae Eukaryota Mature Carpels n.a. n.a. PMID[25116183]
NPO22674 Caulerpa racemosa Species Caulerpaceae Eukaryota n.a. n.a. n.a. PMID[25497963]
NPO24093 Drynaria fortunei Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18853 Alstonia scholaris Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15822 Stypopodium zonale Species Dictyotaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14170 Streptomyces neyagawaensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO22674 Caulerpa racemosa Species Caulerpaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26350 Populus nigra Species Salicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18050 Stilbe ericoides Species Stilbaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28888 Magnaporthe grisea Species Magnaporthaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27088 Oscillatoria nigro-viridis Species Oscillatoriaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO7118 Manglietiastrum sinicum Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24093 Drynaria fortunei Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18853 Alstonia scholaris Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24093 Drynaria fortunei Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18853 Alstonia scholaris Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24093 Drynaria fortunei Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18853 Alstonia scholaris Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24093 Drynaria fortunei Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO24696 Centaurea salicifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7118 Manglietiastrum sinicum Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25799 Lilium martagon Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24093 Drynaria fortunei Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14170 Streptomyces neyagawaensis Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO17903 Nepeta ruderalis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15822 Stypopodium zonale Species Dictyotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26350 Populus nigra Species Salicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17356 Peltigera malacea Species Peltigeraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25759 Drechslera ravenelii Species Pleosporaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18853 Alstonia scholaris Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18050 Stilbe ericoides Species Stilbaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22674 Caulerpa racemosa Species Caulerpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28888 Magnaporthe grisea Species Magnaporthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2290 Clarkia exilis Species Onagraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO27088 Oscillatoria nigro-viridis Species Oscillatoriaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO24324 Halobacterium salinarum Species Halobacteriaceae Archaea n.a. n.a. n.a. Database[UNPD]
NPO11976 Elaeocarpus sikkimensis Species Elaeocarpaceae 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
NPT65 Cell line HepG2 Homo sapiens Activity n.a. n.a. n.a. PMID[34553942]
NPT1397 Cell line INS1 Rattus norvegicus Activity n.a. n.a. n.a. PMID[36781148]

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 NPC166885 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
0.6383 Remote Similarity NPC290550
0.6078 Remote Similarity NPC198260
0.587 Remote Similarity NPC254847
0.5854 Remote Similarity NPC93232
0.5536 Remote Similarity NPC218249
0.5357 Remote Similarity NPC601234
0.5306 Remote Similarity NPC190457
0.5172 Remote Similarity NPC487342
0.5102 Remote Similarity NPC143438
0.5098 Remote Similarity NPC471905
0.5098 Remote Similarity NPC305845
0.5085 Remote Similarity NPC487336
0.5082 Remote Similarity NPC487339

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC166885 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
0.587 Remote Similarity NPD1509 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