Natural Product: NPC54383

Natural Product IDNPC54383
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 NPLTVGMLNDMOQE-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 9879022
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-UHFFFAOYSA-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
SMILES c1cc(ccc1C1CC(=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:   1.896
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.061
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.529
?
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:   0.785 Fluc inhibitor:   0.888
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.255
?
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:   0.548 Promiscuous compounds:   0.118

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.376 MDCK Permeability:   -4.815
Pgp-inhibitor:   0.494 Pgp-substrate:   0.024
PAMPA:   0.8
?
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):   0.007
20% Bioavailability (F20%):   0.036 30% Bioavailability (F30%):   0.923
50% Bioavailability (F50%):   0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.924
Plasma Protein Binding (PPB):   94.586% Volume Distribution (VD):   -0.459
Fu: 4.958%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.968
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.997
BSEP inhibitor:   0.791

ADMET: Metabolism

CYP1A2-inhibitor:   0.132 CYP1A2-substrate:   0.039
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.865
CYP2C9-inhibitor:   0.185 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.751 CYP2D6-substrate:   1.0
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.025
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.743
HLM stability:   0.993
?
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):  9.237 Half-life (T1/2):  1.57

ADMET: Toxicity

hERG Blockers:  0.143 hERG Blockers (10um):  0.75
Human Hepatotoxicity (H-HT):  0.603 Drug-induced Liver Injury (DILI):  0.541
AMES Toxicity:  0.697 Rat Oral Acute Toxicity:  0.532
Maximum Recommended Daily Dose:  0.662 Skin Sensitization:  0.985
Carcinogencity:  0.59 Eye Corrosion:  0.043
Eye Irritation:  0.99 Respiratory Toxicity:  0.445
Drug-induced Neurotoxicity:  0.075 Ototoxicity:  0.656
Hematotoxicity:  0.081 Drug-induced Nephrotoxicity:  0.113
Genotoxicity:  0.946 RPMI-8226 Immunitoxicity:  0.018
A549 Cytotoxicity:  0.82 Hek293 Cytotoxicity:  0.602
BCF:   0.985
?
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:   4.505
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   4.017
?
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
NPO16039 Scutellaria barbata Species Lamiaceae Eukaryota n.a. whole plant n.a. PMID[16755060]
NPO16039 Scutellaria barbata Species Lamiaceae Eukaryota n.a. aerial part n.a. PMID[17666848]
NPO16039 Scutellaria barbata Species Lamiaceae Eukaryota n.a. aerial part n.a. PMID[18239311]
NPO16039 Scutellaria barbata Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[19785430]
NPO28574 Oroxylum indicum Species Bignoniaceae Eukaryota n.a. n.a. n.a. PMID[19948405]
NPO16039 Scutellaria barbata Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[19962306]
NPO16039 Scutellaria barbata Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[20078074]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[22060189]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[22537213]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. flower n.a. PMID[22723874]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[23371463]
NPO28574 Oroxylum indicum Species Bignoniaceae Eukaryota n.a. seed n.a. PMID[23672042]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota Flowers Lasa, China n.a. PMID[24621197]
NPO20278 Scutellaria indica Species Lamiaceae Eukaryota whole plant n.a. n.a. PMID[25637363]
NPO16039 Scutellaria barbata Species Lamiaceae Eukaryota whole plants Nanning District, Guangxi Province, China 2012-Sep PMID[25647077]
NPO16039 Scutellaria barbata Species Lamiaceae Eukaryota aerial parts Seoul, Korea n.a. PMID[26331882]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[27748595]
NPO28574 Oroxylum indicum Species Bignoniaceae Eukaryota n.a. n.a. n.a. PMID[36483735]
NPO11662 Solanum virginianum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[39081888]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[39732883]
NPO31342 Solanum xanthocarpum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20278 Scutellaria indica Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO30253 Duranta repens Species Verbenaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16039 Scutellaria barbata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28574 Oroxylum indicum Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9295 Clerodendron fragrans n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota Oil n.a. n.a. Database[FooDB]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota Flower n.a. n.a. Database[FooDB]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota Bud n.a. n.a. Database[FooDB]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. Database[FooDB]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. Database[FooDB]
NPO31342 Solanum xanthocarpum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16039 Scutellaria barbata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO5788 Millingtonia hortensis Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20278 Scutellaria indica Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30253 Duranta repens Species Verbenaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9295 Clerodendron fragrans n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO28574 Oroxylum indicum Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28574 Oroxylum indicum Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16039 Scutellaria barbata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11662 Solanum virginianum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5788 Millingtonia hortensis Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9295 Clerodendron fragrans n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO20278 Scutellaria indica Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16039 Scutellaria barbata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO20278 Scutellaria indica Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9295 Clerodendron fragrans n.a. n.a. n.a. n.a. n.a. n.a. Database[TCM_Taiwan]
NPO5788 Millingtonia hortensis Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28574 Oroxylum indicum Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30253 Duranta repens Species Verbenaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO31342 Solanum xanthocarpum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO16039 Scutellaria barbata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28574 Oroxylum indicum Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28574 Oroxylum indicum Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11662 Solanum virginianum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5788 Millingtonia hortensis Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20278 Scutellaria indica Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18311 Carthamus tinctorius Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16039 Scutellaria barbata Species Lamiaceae 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 NPC54383 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 NPC54383 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