Natural Product: NPC208380

Natural Product IDNPC208380
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 GFZFUVWXGQWUGX-ZICOWINBSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 14353342
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000476] Cinnamic acids and derivatives
        • [CHEMONTID:0001391] Hydroxycinnamic acids and derivatives
          • [CHEMONTID:0000059] Coumaric 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 GFZFUVWXGQWUGX-ZICOWINBSA-N
Standard InCHI InChI=1S/C17H14O6/c18-13-4-1-11(9-15(13)20)3-6-17(22)23-8-7-12-2-5-14(19)16(21)10-12/h1-10,18-21H/b6-3+,8-7+
SMILES c1cc(c(cc1/C=C/C(=O)O/C=C/c1ccc(c(c1)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   314.08 Volume:   314.489
?
Van der Waals volume.
Dense:   0.999 LogP:   2.105
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.175
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.258
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   5.0 Rigid Bonds:   15.0
TPSA:   107.22
?
Topological Polar Surface Area.
 H-Bond Acceptor:   6.0
H-Bond Donor:   4.0 Rings:   2.0
Heavy Atoms:   6.0

MedChem Properties

QED Drug-Likeness Score:   0.299 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.633 Fsp3:   0.0
MCE-18:   13.0
?
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:   0.992 Fluc inhibitor:   1.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.198
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.523
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.864 Promiscuous compounds:   0.865

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.478 MDCK Permeability:   -4.84
Pgp-inhibitor:   0.0 Pgp-substrate:   0.001
PAMPA:   0.62
?
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):   0.074
20% Bioavailability (F20%):   0.997 30% Bioavailability (F30%):   0.997
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.007 MRP1:   0.141
Plasma Protein Binding (PPB):   89.98% Volume Distribution (VD):   -0.279
Fu: 11.773%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.996
OATP1B3 inhibitor:   0.999 BCRP inhibitor:   0.066
BSEP inhibitor:   0.038

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.05
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.001 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.011 CYP2D6-substrate:   0.252
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.394
?
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):  17.531 Half-life (T1/2):  1.647

ADMET: Toxicity

hERG Blockers:  0.104 hERG Blockers (10um):  0.834
Human Hepatotoxicity (H-HT):  0.288 Drug-induced Liver Injury (DILI):  0.77
AMES Toxicity:  0.741 Rat Oral Acute Toxicity:  0.209
Maximum Recommended Daily Dose:  0.758 Skin Sensitization:  1.0
Carcinogencity:  0.365 Eye Corrosion:  0.059
Eye Irritation:  0.979 Respiratory Toxicity:  0.09
Drug-induced Neurotoxicity:  0.027 Ototoxicity:  0.595
Hematotoxicity:  0.017 Drug-induced Nephrotoxicity:  0.058
Genotoxicity:  0.685 RPMI-8226 Immunitoxicity:  0.01
A549 Cytotoxicity:  0.882 Hek293 Cytotoxicity:  0.383
BCF:   1.241
?
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:   4.348
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.537
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.322
?
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
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s11356-018-3422-z]
NPO2257 Oceanapia phillipensis Species Phloeodictyidae Eukaryota n.a. n.a. n.a. PMID[10654417]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. n.a. PMID[15516765]
NPO10996 Ferula assa-foetida Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[19691312]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. n.a. PMID[20973550]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. n.a. PMID[23700450]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. leaf n.a. PMID[23849114]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. n.a. PMID[24310066]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. seed n.a. PMID[25433632]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. seed n.a. PMID[26860358]
NPO10996 Ferula assa-foetida Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[31707845]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. PMID[31861466]
NPO10996 Ferula assa-foetida Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[385653815]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. n.a. PMID[38792127]
NPO1638 Ulmus laciniata Species Ulmaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10996 Ferula assa-foetida Species Apiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11235 Asplenium nidus Species Aspleniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29219 Primula veris Species Primulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14797 Orthosiphon aristatus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5890 Astragalus inopinatus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2499 Celmisia petriei Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO592 Chroogomphus rutilus Species Gomphidiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1408 Cirsium helenioides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10073 Clusia torresii Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14887 Handroanthus guayacan Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2257 Oceanapia phillipensis Species Phloeodictyidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5511 Populus tremula Species Salicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8981 Senecio integerrimus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8541 Oryza sativa Species Poaceae Eukaryota Petiole n.a. n.a. Database[FooDB]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. Database[FooDB]
NPO8541 Oryza sativa Species Poaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO8541 Oryza sativa Species Poaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO8541 Oryza sativa Species Poaceae Eukaryota Protoplast n.a. n.a. Database[FooDB]
NPO8541 Oryza sativa Species Poaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO8541 Oryza sativa Species Poaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. Database[FooDB]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29219 Primula veris Species Primulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5511 Populus tremula Species Salicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8981 Senecio integerrimus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. seed n.a. Database[MetaboLights]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5511 Populus tremula Species Salicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8981 Senecio integerrimus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29219 Primula veris Species Primulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO14797 Orthosiphon aristatus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8541 Oryza sativa Species Poaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO592 Chroogomphus rutilus Species Gomphidiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29219 Primula veris Species Primulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11235 Asplenium nidus Species Aspleniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10073 Clusia torresii Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8981 Senecio integerrimus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2257 Oceanapia phillipensis Species Phloeodictyidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10996 Ferula assa-foetida Species Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1638 Ulmus laciniata Species Ulmaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14887 Handroanthus guayacan Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5890 Astragalus inopinatus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5511 Populus tremula Species Salicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1408 Cirsium helenioides Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2499 Celmisia petriei 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 NPC208380 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 NPC150610
0.6923 Remote Similarity NPC226250
0.6429 Remote Similarity NPC95381
0.6 Remote Similarity NPC217472
0.5745 Remote Similarity NPC233669
0.5745 Remote Similarity NPC275519
0.5745 Remote Similarity NPC261453
0.5745 Remote Similarity NPC217052
0.5745 Remote Similarity NPC474967
0.5745 Remote Similarity NPC329344
0.5745 Remote Similarity NPC237506
0.5745 Remote Similarity NPC32626
0.5745 Remote Similarity NPC33749
0.5625 Remote Similarity NPC147654
0.5625 Remote Similarity NPC281277
0.551 Remote Similarity NPC328593
0.551 Remote Similarity NPC474275
0.551 Remote Similarity NPC147192
0.551 Remote Similarity NPC309434
0.551 Remote Similarity NPC224208
0.551 Remote Similarity NPC41661
0.54 Remote Similarity NPC263386
0.54 Remote Similarity NPC141791
0.5385 Remote Similarity NPC251407
0.5385 Remote Similarity NPC168653
0.5294 Remote Similarity NPC203124
0.5294 Remote Similarity NPC607366
0.5192 Remote Similarity NPC65791
0.5192 Remote Similarity NPC132921
0.5192 Remote Similarity NPC168799
0.5192 Remote Similarity NPC106406
0.5122 Remote Similarity NPC19149
0.5116 Remote Similarity NPC253746
0.5111 Remote Similarity NPC94343
0.5094 Remote Similarity NPC470849
0.5094 Remote Similarity NPC488563
0.5094 Remote Similarity NPC474895

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC208380 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