Natural Product: NPC43212

Natural Product IDNPC43212
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 DJSISFGPUUYILV-ZFORQUDYSA-M
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 29927686
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0001111] Flavonoid glycosides
          • [CHEMONTID:0001583] Flavonoid O-glycosides
            • [CHEMONTID:0002934] Flavonoid O-glucuronides
              • [CHEMONTID:0003534] Flavonoid-7-O-glucuronides

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 DJSISFGPUUYILV-ZFORQUDYSA-M
Standard InCHI InChI=1S/C21H18O12/c22-8-3-1-7(2-4-8)10-5-9(23)13-11(31-10)6-12(14(24)15(13)25)32-21-18(28)16(26)17(27)19(33-21)20(29)30/h1-6,16-19,21-22,24-28H,(H,29,30)/p-1/t16-,17-,18+,19-,21+/m0/s1
SMILES c1cc(ccc1c1cc(=O)c2c(cc(c(c2O)O)O[C@H]2[C@@H]([C@H]([C@@H]([C@@H](C(=O)O)O2)O)O)O)o1)[O-]

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   462.08 Volume:   419.301
?
Van der Waals volume.
Dense:   1.102 LogP:   0.894
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.232
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -2.908
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   25.0
TPSA:   207.35
?
Topological Polar Surface Area.
 H-Bond Acceptor:   12.0
H-Bond Donor:   7.0 Rings:   4.0
Heavy Atoms:   12.0

MedChem Properties

QED Drug-Likeness Score:   0.253 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.997 Fsp3:   0.238
MCE-18:   91.385
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Accepted
Pfizer Rule:   Rejected GSK Rule:   Accepted
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   1 PAINS Alert:   1
Colloidal aggregators:   0.392 Fluc inhibitor:   0.334
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.938
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.883
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.29 Promiscuous compounds:   0.473

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.65 MDCK Permeability:   -5.038
Pgp-inhibitor:   0.0 Pgp-substrate:   0.466
PAMPA:   1.0
?
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):   0.04
20% Bioavailability (F20%):   0.349 30% Bioavailability (F30%):   0.703
50% Bioavailability (F50%):   0.95

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.904
Plasma Protein Binding (PPB):   82.786% Volume Distribution (VD):   0.016
Fu: 13.646%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.017
OATP1B3 inhibitor:   0.031 BCRP inhibitor:   0.137
BSEP inhibitor:   0.002

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.01 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.001 CYP2D6-substrate:   0.003
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.003
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.781
HLM stability:   0.003
?
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):  1.908 Half-life (T1/2):  3.717

ADMET: Toxicity

hERG Blockers:  0.009 hERG Blockers (10um):  0.054
Human Hepatotoxicity (H-HT):  0.398 Drug-induced Liver Injury (DILI):  0.917
AMES Toxicity:  0.487 Rat Oral Acute Toxicity:  0.094
Maximum Recommended Daily Dose:  0.125 Skin Sensitization:  0.972
Carcinogencity:  0.046 Eye Corrosion:  0.0
Eye Irritation:  0.862 Respiratory Toxicity:  0.062
Drug-induced Neurotoxicity:  0.003 Ototoxicity:  0.532
Hematotoxicity:  0.076 Drug-induced Nephrotoxicity:  0.462
Genotoxicity:  0.9 RPMI-8226 Immunitoxicity:  0.104
A549 Cytotoxicity:  0.181 Hek293 Cytotoxicity:  0.234
BCF:   0.179
?
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:   2.731
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.032
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.34
?
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
NPO6473.1 Perilla frutescens var. acuta Strain Lamiaceae Eukaryota n.a. n.a. n.a. PMID[10757731]
NPO21324 Plantago major Species Plantaginaceae Eukaryota Whole Plant the surroundings of Uppsala, Sweden 1998-SEP PMID[11421736]
NPO21324 Plantago major Species Plantaginaceae Eukaryota Entire plants the surroundings of Uppsala, Sweden 1998-SEP PMID[11421736]
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]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[19829679]
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]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. root n.a. PMID[21087019]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[22314230]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[23521110]
NPO28574 Oroxylum indicum Species Bignoniaceae Eukaryota n.a. seed n.a. PMID[23672042]
NPO21324 Plantago major Species Plantaginaceae Eukaryota n.a. seed n.a. PMID[24895551]
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]
NPO9809 Scutellaria altissima Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[32772473]
NPO28574 Oroxylum indicum Species Bignoniaceae Eukaryota n.a. n.a. n.a. PMID[36483735]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[37569279]
NPO21324 Plantago major Species Plantaginaceae Eukaryota n.a. n.a. n.a. PMID[9784154]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[9834167]
NPO9809 Scutellaria altissima Species Lamiaceae 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]
NPO8650.1 Perilla frutescens var. arguta Varieties Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16039 Scutellaria barbata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9153 Sorbaria sorbifolia Species Rosaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28877 Scutellaria baicalensis 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]
NPO21324 Plantago major Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6473.1 Perilla frutescens var. acuta Strain Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9809 Scutellaria altissima Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8650.1 Perilla frutescens var. arguta Varieties Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4014 Erigeron breviscapus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21324 Plantago major Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28300 Sorbaria arborea Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6473.1 Perilla frutescens var. acuta Strain Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16039 Scutellaria barbata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9153 Sorbaria sorbifolia Species Rosaceae 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]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4014 Erigeron breviscapus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28300 Sorbaria arborea Species Rosaceae 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]
NPO16039 Scutellaria barbata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8650.1 Perilla frutescens var. arguta Varieties Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9153 Sorbaria sorbifolia Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9809 Scutellaria altissima Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28574 Oroxylum indicum Species Bignoniaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21324 Plantago major Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6473.1 Perilla frutescens var. acuta Strain Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28300 Sorbaria arborea Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28877 Scutellaria baicalensis Species Lamiaceae 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]
NPO21324 Plantago major Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16039 Scutellaria barbata 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]
NPO9153 Sorbaria sorbifolia Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16039 Scutellaria barbata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28877 Scutellaria baicalensis 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]
NPO4014 Erigeron breviscapus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4014 Erigeron breviscapus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28300 Sorbaria arborea Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9153 Sorbaria sorbifolia Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8650.1 Perilla frutescens var. arguta Varieties Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21324 Plantago major Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9809 Scutellaria altissima Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28574 Oroxylum indicum Species Bignoniaceae 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 NPC43212 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
0.8649 High Similarity NPC237435
0.8533 High Similarity NPC43211
0.7821 Intermediate Similarity NPC115760
0.6951 Remote Similarity NPC608742
0.6627 Remote Similarity NPC282169
0.6512 Remote Similarity NPC600989
0.6429 Remote Similarity NPC20505
0.593 Remote Similarity NPC101191
0.5862 Remote Similarity NPC210094
0.5765 Remote Similarity NPC45618
0.5698 Remote Similarity NPC146792
0.5682 Remote Similarity NPC135277
0.5632 Remote Similarity NPC58716
0.5467 Remote Similarity NPC57030
0.5275 Remote Similarity NPC264735
0.5256 Remote Similarity NPC283600
0.5132 Remote Similarity NPC275722
0.5128 Remote Similarity NPC212678
0.5065 Remote Similarity NPC198826
0.5062 Remote Similarity NPC485299

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC43212 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
0.8649 High Similarity NPD4338 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