Natural Product: NPC119092

Natural Product IDNPC119092
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 NPLTVGMLNDMOQE-LLVKDONJSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0000337] Flavans
          • [CHEMONTID:0001632] Flavanones

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 NPLTVGMLNDMOQE-LLVKDONJSA-N
Standard InCHI InChI=1S/C15H12O6/c16-8-3-1-7(2-4-8)11-5-9(17)13-12(21-11)6-10(18)14(19)15(13)20/h1-4,6,11,16,18-20H,5H2/t11-/m1/s1
SMILES c1cc(ccc1[C@H]1CC(=O)c2c(cc(c(c2O)O)O)O1)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   288.06 Volume:   276.613
?
Van der Waals volume.
Dense:   1.041 LogP:   2.095
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.183
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.799
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   1.0 Rigid Bonds:   18.0
TPSA:   107.22
?
Topological Polar Surface Area.
 H-Bond Acceptor:   6.0
H-Bond Donor:   4.0 Rings:   3.0
Heavy Atoms:   6.0

MedChem Properties

QED Drug-Likeness Score:   0.599 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.971 Fsp3:   0.133
MCE-18:   58.235
?
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:   0.748 Fluc inhibitor:   0.574
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.21
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.155
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.556 Promiscuous compounds:   0.137

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.332 MDCK Permeability:   -4.816
Pgp-inhibitor:   0.07 Pgp-substrate:   0.067
PAMPA:   0.603
?
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):   0.001
20% Bioavailability (F20%):   0.058 30% Bioavailability (F30%):   0.905
50% Bioavailability (F50%):   0.995

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.946
Plasma Protein Binding (PPB):   93.929% Volume Distribution (VD):   -0.465
Fu: 6.154%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.774
OATP1B3 inhibitor:   0.993 BCRP inhibitor:   0.992
BSEP inhibitor:   0.365

ADMET: Metabolism

CYP1A2-inhibitor:   0.011 CYP1A2-substrate:   0.02
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.803
CYP2C9-inhibitor:   0.006 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.098 CYP2D6-substrate:   0.973
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.956
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.977
HLM stability:   0.96
?
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):  11.986 Half-life (T1/2):  1.653

ADMET: Toxicity

hERG Blockers:  0.127 hERG Blockers (10um):  0.686
Human Hepatotoxicity (H-HT):  0.705 Drug-induced Liver Injury (DILI):  0.689
AMES Toxicity:  0.704 Rat Oral Acute Toxicity:  0.66
Maximum Recommended Daily Dose:  0.782 Skin Sensitization:  0.995
Carcinogencity:  0.348 Eye Corrosion:  0.16
Eye Irritation:  0.995 Respiratory Toxicity:  0.734
Drug-induced Neurotoxicity:  0.253 Ototoxicity:  0.683
Hematotoxicity:  0.055 Drug-induced Nephrotoxicity:  0.191
Genotoxicity:  0.992 RPMI-8226 Immunitoxicity:  0.021
A549 Cytotoxicity:  0.94 Hek293 Cytotoxicity:  0.48
BCF:   1.004
?
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:   3.601
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.537
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.055
?
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
NPO13968 Garcinia scortechinii Species Clusiaceae Eukaryota fruits n.a. n.a. PMID[16038540]
NPO14358 Rhodobacter sphaeroides Species Rhodobacteraceae Bacteria n.a. n.a. n.a. PMID[1612412]
NPO8068 Blumea mollis Species Asteraceae Eukaryota n.a. leaf n.a. PMID[18566831]
NPO14162 Chlorophytum borivilianum Species Asparagaceae Eukaryota roots n.a. n.a. PMID[19128156]
NPO7016 Gardenia tubifera Species Rubiaceae Eukaryota exudate n.a. n.a. PMID[20028108]
NPO12357 Lycopus europaeus Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[20674349]
NPO11492 Kopsia grandifolia Species Apocynaceae Eukaryota n.a. leaf n.a. PMID[21428274]
NPO11492 Kopsia grandifolia Species Apocynaceae Eukaryota n.a. stem n.a. PMID[21428274]
NPO8650 Perilla frutescens Species Lamiaceae Eukaryota leaves n.a. n.a. PMID[22272932]
NPO8650 Perilla frutescens Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[25320841]
NPO1795 Fragaria vesca Species Rosaceae Eukaryota n.a. fruit n.a. PMID[26169681]
NPO3465 Aconitum leucostomum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13467 Anarsia lineatella Species Gelechiidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14358 Rhodobacter sphaeroides Species Rhodobacteraceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO8650 Perilla frutescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14057 Apollonias barbujana Species Lauraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4004 Aquilegia ecalcarata Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8068 Blumea mollis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10550 Artemisia hanseniana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14162 Chlorophytum borivilianum Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8892 Sordaria araneosa Species Sordariaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4671 Persea mexicana Species Lauraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5191 Penicillium cinerascens Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO746 Panax innovans Species Araliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12357 Lycopus europaeus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11998 Ledebouria socialis Species Hyacinthaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO205 Lasianthus fordii Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11492 Kopsia grandifolia Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16703 Isodon lophanthoides Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13014 Ipomoea cairica Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7016 Gardenia tubifera Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13968 Garcinia scortechinii Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1795 Fragaria vesca Species Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12509 Dipterocarpus dyeri Species Dipterocarpaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13766 Ceanothus velutinus Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13014 Ipomoea cairica Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1795 Fragaria vesca Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12357 Lycopus europaeus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8650 Perilla frutescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13968 Garcinia scortechinii Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4004 Aquilegia ecalcarata Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16703 Isodon lophanthoides Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3465 Aconitum leucostomum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8650 Perilla frutescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12357 Lycopus europaeus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13014 Ipomoea cairica Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1795 Fragaria vesca Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13014 Ipomoea cairica Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8650 Perilla frutescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3465 Aconitum leucostomum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8650 Perilla frutescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11492 Kopsia grandifolia Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16703 Isodon lophanthoides Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14057 Apollonias barbujana Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1795 Fragaria vesca Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4004 Aquilegia ecalcarata Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13766 Ceanothus velutinus Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13968 Garcinia scortechinii Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14358 Rhodobacter sphaeroides Species Rhodobacteraceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO8892 Sordaria araneosa Species Sordariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3465 Aconitum leucostomum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4671 Persea mexicana Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8650 Perilla frutescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11998 Ledebouria socialis Species Hyacinthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO746 Panax innovans Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12357 Lycopus europaeus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10550 Artemisia hanseniana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13467 Anarsia lineatella Species Gelechiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14162 Chlorophytum borivilianum Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12509 Dipterocarpus dyeri Species Dipterocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13014 Ipomoea cairica Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7016 Gardenia tubifera Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO205 Lasianthus fordii Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8068 Blumea mollis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5191 Penicillium cinerascens Species Aspergillaceae 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 NPC119092 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
0.8043 Intermediate Similarity NPC204515
0.6939 Remote Similarity NPC32441
0.6939 Remote Similarity NPC79943
0.6667 Remote Similarity NPC300668
0.6667 Remote Similarity NPC324386
0.6538 Remote Similarity NPC606248
0.6346 Remote Similarity NPC329203
0.6346 Remote Similarity NPC222342
0.6327 Remote Similarity NPC329225
0.6327 Remote Similarity NPC147686
0.6078 Remote Similarity NPC225153
0.6078 Remote Similarity NPC479876
0.6038 Remote Similarity NPC201837
0.5932 Remote Similarity NPC470135
0.5926 Remote Similarity NPC321011
0.5926 Remote Similarity NPC294852
0.5926 Remote Similarity NPC469764
0.5926 Remote Similarity NPC188679
0.5926 Remote Similarity NPC475267
0.566 Remote Similarity NPC243083
0.566 Remote Similarity NPC13768
0.566 Remote Similarity NPC287246
0.566 Remote Similarity NPC603284
0.5574 Remote Similarity NPC134171
0.5556 Remote Similarity NPC1612
0.5556 Remote Similarity NPC183959
0.5556 Remote Similarity NPC167624
0.5556 Remote Similarity NPC166482
0.5517 Remote Similarity NPC236637
0.5472 Remote Similarity NPC476480
0.5472 Remote Similarity NPC84585
0.5455 Remote Similarity NPC274784
0.5455 Remote Similarity NPC20709
0.541 Remote Similarity NPC470131
0.541 Remote Similarity NPC470133
0.541 Remote Similarity NPC470132
0.537 Remote Similarity NPC295261
0.537 Remote Similarity NPC296490
0.5357 Remote Similarity NPC485881
0.5357 Remote Similarity NPC210084
0.5345 Remote Similarity NPC474836
0.5273 Remote Similarity NPC312391
0.5246 Remote Similarity NPC69674
0.5246 Remote Similarity NPC477841
0.5231 Remote Similarity NPC69531
0.5231 Remote Similarity NPC611447
0.5185 Remote Similarity NPC182421
0.5179 Remote Similarity NPC255106
0.5179 Remote Similarity NPC482119
0.5179 Remote Similarity NPC235165
0.5179 Remote Similarity NPC482120
0.5161 Remote Similarity NPC220998
0.5152 Remote Similarity NPC51760
0.5147 Remote Similarity NPC488556
0.5091 Remote Similarity NPC264083
0.5091 Remote Similarity NPC6407
0.5091 Remote Similarity NPC545184
0.5082 Remote Similarity NPC39329
0.5082 Remote Similarity NPC51032
0.5082 Remote Similarity NPC39045
0.5079 Remote Similarity NPC486094
0.5075 Remote Similarity NPC228504

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC119092 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
0.6939 Remote Similarity NPD1552 Clinical (unspecified phase)
0.6327 Remote Similarity NPD1549 Phase 2
0.566 Remote Similarity NPD1550 Phase 2

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