Natural Product: NPC159087

Natural Product IDNPC159087
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 OZVBXGBZPZBKJO-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 5320181
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0002585] O-methylated flavonoids
          • [CHEMONTID:0002595] 3'-O-methylated flavonoids

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 OZVBXGBZPZBKJO-UHFFFAOYSA-N
Standard InCHI InChI=1S/C16H12O7/c1-22-12-4-7(2-3-8(12)17)11-5-9(18)14-13(23-11)6-10(19)15(20)16(14)21/h2-6,17,19-21H,1H3
SMILES COc1cc(ccc1O)c1cc(=O)c2c(cc(c(c2O)O)O)o1

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   316.06 Volume:   300.063
?
Van der Waals volume.
Dense:   1.053 LogP:   2.039
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.98
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.225
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   2.0 Rigid Bonds:   18.0
TPSA:   120.36
?
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:   0.535 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.464 Fsp3:   0.062
MCE-18:   19.0
?
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:   0.861 Fluc inhibitor:   0.764
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.944
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.646
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.573 Promiscuous compounds:   0.901

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.099 MDCK Permeability:   -4.772
Pgp-inhibitor:   0.033 Pgp-substrate:   0.105
PAMPA:   0.491
?
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):   0.038
20% Bioavailability (F20%):   0.758 30% Bioavailability (F30%):   0.916
50% Bioavailability (F50%):   0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.001 MRP1:   0.954
Plasma Protein Binding (PPB):   96.901% Volume Distribution (VD):   -0.449
Fu: 2.906%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.99
OATP1B3 inhibitor:   0.999 BCRP inhibitor:   0.995
BSEP inhibitor:   0.606

ADMET: Metabolism

CYP1A2-inhibitor:   0.002 CYP1A2-substrate:   0.04
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.001
CYP2C9-inhibitor:   0.618 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.998 CYP2D6-substrate:   1.0
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.004
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.271
?
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):  8.12 Half-life (T1/2):  1.521

ADMET: Toxicity

hERG Blockers:  0.067 hERG Blockers (10um):  0.674
Human Hepatotoxicity (H-HT):  0.354 Drug-induced Liver Injury (DILI):  0.775
AMES Toxicity:  0.684 Rat Oral Acute Toxicity:  0.411
Maximum Recommended Daily Dose:  0.795 Skin Sensitization:  0.988
Carcinogencity:  0.598 Eye Corrosion:  0.546
Eye Irritation:  0.996 Respiratory Toxicity:  0.684
Drug-induced Neurotoxicity:  0.007 Ototoxicity:  0.355
Hematotoxicity:  0.047 Drug-induced Nephrotoxicity:  0.015
Genotoxicity:  0.965 RPMI-8226 Immunitoxicity:  0.016
A549 Cytotoxicity:  0.819 Hek293 Cytotoxicity:  0.46
BCF:   0.772
?
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:   3.381
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.24
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.813
?
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
NPO22874 Bombyx mori Species Bombycidae Eukaryota n.a. n.a. n.a. PMID[18071251]
NPO22874 Bombyx mori Species Bombycidae Eukaryota n.a. faeces n.a. PMID[18323202]
NPO25456 Cortinarius infractus Species Cortinariaceae Eukaryota Toadstool n.a. n.a. PMID[20176490]
NPO25579 Alstonia pneumatophora Species Apocynaceae Eukaryota n.a. n.a. n.a. PMID[20576577]
NPO10051 Phyla nodiflora Species Verbenaceae Eukaryota n.a. aerial part n.a. PMID[25140335]
NPO2392 Hansenia weberbaueriana Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[25333853]
NPO10051 Phyla nodiflora Species Verbenaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19968 Millettia ovalifolia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4340 Peucedanum praeruptorum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2392 Hansenia weberbaueriana Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24644 Hansenia forbesii Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22874 Bombyx mori Species Bombycidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25579 Alstonia pneumatophora Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25456 Cortinarius infractus Species Cortinariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO30681 Lippia nodiflora Species Verbenaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24451 Gaylussacia frondosa Species Ericaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23338 Cribrochalina dura Species Niphatidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24861 Usnea aciculifera Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24959 Chaenomeles cathayensis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19268 Climacostomum virens Species Climacostomidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24761 Enicostema littorale Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24904 Mangifera gabonensis Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25688 Mikania congesta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25551 Monodora grandiflora Species Annonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8634 Podocarpus mannii Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25270 Trichoderma roseum Species Hypocreaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO25066 Werneria stuebelii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO22874 Bombyx mori Species Bombycidae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30681 Lippia nodiflora Species Verbenaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4340 Peucedanum praeruptorum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24644 Hansenia forbesii Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22874 Bombyx mori Species Bombycidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10051 Phyla nodiflora Species Verbenaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4340 Peucedanum praeruptorum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2392 Hansenia weberbaueriana Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22874 Bombyx mori Species Bombycidae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4340 Peucedanum praeruptorum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30681 Lippia nodiflora Species Verbenaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2392 Hansenia weberbaueriana Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO4340 Peucedanum praeruptorum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO24644 Hansenia forbesii Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO24761 Enicostema littorale Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25688 Mikania congesta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24451 Gaylussacia frondosa Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25456 Cortinarius infractus Species Cortinariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25579 Alstonia pneumatophora Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19968 Millettia ovalifolia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25066 Werneria stuebelii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24959 Chaenomeles cathayensis Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22874 Bombyx mori Species Bombycidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19268 Climacostomum virens Species Climacostomidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4340 Peucedanum praeruptorum Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24904 Mangifera gabonensis Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8634 Podocarpus mannii Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23338 Cribrochalina dura Species Niphatidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25551 Monodora grandiflora Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24861 Usnea aciculifera Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24644 Hansenia forbesii Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20993 Bystropogon mollis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10051 Phyla nodiflora Species Verbenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25270 Trichoderma roseum Species Hypocreaceae 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 NPC159087 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
0.75 Intermediate Similarity NPC83508
0.7241 Intermediate Similarity NPC183950
0.7143 Intermediate Similarity NPC184136
0.6852 Remote Similarity NPC130230
0.6852 Remote Similarity NPC275772
0.6724 Remote Similarity NPC312924
0.6667 Remote Similarity NPC47781
0.6667 Remote Similarity NPC137062
0.65 Remote Similarity NPC128863
0.65 Remote Similarity NPC115323
0.6364 Remote Similarity NPC239312
0.6333 Remote Similarity NPC280339
0.6333 Remote Similarity NPC20830
0.6269 Remote Similarity NPC602497
0.623 Remote Similarity NPC4455
0.6129 Remote Similarity NPC227325
0.6129 Remote Similarity NPC606105
0.6 Remote Similarity NPC100887
0.5902 Remote Similarity NPC162313
0.5833 Remote Similarity NPC241498
0.5833 Remote Similarity NPC284552
0.5806 Remote Similarity NPC167815
0.5738 Remote Similarity NPC214138
0.5738 Remote Similarity NPC198826
0.56 Remote Similarity NPC475942
0.5556 Remote Similarity NPC255350
0.5484 Remote Similarity NPC120464
0.5469 Remote Similarity NPC283600
0.541 Remote Similarity NPC293183
0.5397 Remote Similarity NPC256283
0.5385 Remote Similarity NPC125062
0.5385 Remote Similarity NPC111249
0.5385 Remote Similarity NPC279989
0.5323 Remote Similarity NPC275722
0.5323 Remote Similarity NPC156222
0.5312 Remote Similarity NPC212678
0.5238 Remote Similarity NPC57030
0.5231 Remote Similarity NPC18607
0.5231 Remote Similarity NPC52005
0.5231 Remote Similarity NPC12200
0.5224 Remote Similarity NPC485299
0.5156 Remote Similarity NPC108406
0.5156 Remote Similarity NPC25270
0.5152 Remote Similarity NPC252933
0.5075 Remote Similarity NPC227192

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC159087 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
0.5556 Remote Similarity NPD2801 Pre-clinical

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