Natural Product: NPC121886

Natural Product IDNPC121886
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 USQXPEWRYWRRJD-LBPRGKRZSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 440836
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 USQXPEWRYWRRJD-LBPRGKRZSA-N
Standard InCHI InChI=1S/C15H12O7/c16-7-3-8(17)14-9(18)5-12(22-13(14)4-7)6-1-10(19)15(21)11(20)2-6/h1-4,12,16-17,19-21H,5H2/t12-/m0/s1
SMILES c1c(cc(c(c1O)O)O)[C@@H]1CC(=O)c2c(cc(cc2O1)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   304.06 Volume:   285.403
?
Van der Waals volume.
Dense:   1.065 LogP:   1.764
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.85
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -3.681
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   1.0 Rigid Bonds:   18.0
TPSA:   127.45
?
Topological Polar Surface Area.
 H-Bond Acceptor:   7.0
H-Bond Donor:   5.0 Rings:   3.0
Heavy Atoms:   7.0

MedChem Properties

QED Drug-Likeness Score:   0.509 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.174 Fsp3:   0.133
MCE-18:   61.471
?
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:   0.808 Fluc inhibitor:   0.388
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.199
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.245
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.539 Promiscuous compounds:   0.119

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.766 MDCK Permeability:   -4.902
Pgp-inhibitor:   0.119 Pgp-substrate:   0.025
PAMPA:   0.671
?
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):   0.019
20% Bioavailability (F20%):   0.14 30% Bioavailability (F30%):   0.997
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.001 MRP1:   0.856
Plasma Protein Binding (PPB):   92.578% Volume Distribution (VD):   -0.405
Fu: 6.905%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.996
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.995
BSEP inhibitor:   0.064

ADMET: Metabolism

CYP1A2-inhibitor:   0.643 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.7
CYP2C9-inhibitor:   0.056 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.995
CYP3A4-inhibitor:   0.001 CYP3A4-substrate:   0.998
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.996
HLM stability:   0.775
?
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):  8.792 Half-life (T1/2):  1.65

ADMET: Toxicity

hERG Blockers:  0.062 hERG Blockers (10um):  0.744
Human Hepatotoxicity (H-HT):  0.502 Drug-induced Liver Injury (DILI):  0.721
AMES Toxicity:  0.812 Rat Oral Acute Toxicity:  0.498
Maximum Recommended Daily Dose:  0.856 Skin Sensitization:  0.996
Carcinogencity:  0.552 Eye Corrosion:  0.018
Eye Irritation:  0.997 Respiratory Toxicity:  0.475
Drug-induced Neurotoxicity:  0.013 Ototoxicity:  0.721
Hematotoxicity:  0.027 Drug-induced Nephrotoxicity:  0.032
Genotoxicity:  0.998 RPMI-8226 Immunitoxicity:  0.017
A549 Cytotoxicity:  0.973 Hek293 Cytotoxicity:  0.631
BCF:   1.007
?
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:   3.543
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.657
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.907
?
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
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[19829679]
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]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[37569279]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[9834167]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28877 Scutellaria baicalensis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28877 Scutellaria baicalensis 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[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 NPC121886 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
0.8409 Intermediate Similarity NPC182421
0.8085 Intermediate Similarity NPC321011
0.8085 Intermediate Similarity NPC294852
0.8085 Intermediate Similarity NPC188679
0.7447 Intermediate Similarity NPC32441
0.7447 Intermediate Similarity NPC243083
0.7447 Intermediate Similarity NPC13768
0.7447 Intermediate Similarity NPC287246
0.7447 Intermediate Similarity NPC79943
0.7143 Intermediate Similarity NPC274784
0.7143 Intermediate Similarity NPC338131
0.7143 Intermediate Similarity NPC20709
0.7059 Intermediate Similarity NPC302950
0.6786 Remote Similarity NPC106976
0.6735 Remote Similarity NPC295261
0.6735 Remote Similarity NPC296490
0.6735 Remote Similarity NPC12296
0.6481 Remote Similarity NPC236637
0.6471 Remote Similarity NPC107586
0.6364 Remote Similarity NPC258630
0.6167 Remote Similarity NPC470890
0.6154 Remote Similarity NPC73028
0.6154 Remote Similarity NPC19721
0.614 Remote Similarity NPC477841
0.6102 Remote Similarity NPC174953
0.6034 Remote Similarity NPC17170
0.6034 Remote Similarity NPC109223
0.6034 Remote Similarity NPC10937
0.6 Remote Similarity NPC74924
0.6 Remote Similarity NPC134783
0.5833 Remote Similarity NPC108456
0.5806 Remote Similarity NPC473990
0.5714 Remote Similarity NPC118256
0.5645 Remote Similarity NPC312973
0.5645 Remote Similarity NPC200761
0.5645 Remote Similarity NPC475790
0.5625 Remote Similarity NPC474021
0.5556 Remote Similarity NPC611447
0.5472 Remote Similarity NPC264083
0.5472 Remote Similarity NPC204515
0.5455 Remote Similarity NPC224851
0.5455 Remote Similarity NPC474038
0.5385 Remote Similarity NPC473272
0.537 Remote Similarity NPC1612
0.537 Remote Similarity NPC183959
0.5323 Remote Similarity NPC85121
0.5312 Remote Similarity NPC69531
0.5273 Remote Similarity NPC329203
0.5273 Remote Similarity NPC324386
0.5273 Remote Similarity NPC222342
0.5224 Remote Similarity NPC26195
0.5185 Remote Similarity NPC6407
0.5185 Remote Similarity NPC545184
0.5179 Remote Similarity NPC469764
0.5147 Remote Similarity NPC227579
0.5147 Remote Similarity NPC214166
0.5147 Remote Similarity NPC475784
0.5091 Remote Similarity NPC150648
0.5091 Remote Similarity NPC312391
0.5088 Remote Similarity NPC18727
0.5088 Remote Similarity NPC310135
0.5088 Remote Similarity NPC36835
0.5088 Remote Similarity NPC246162
0.5088 Remote Similarity NPC9743
0.5088 Remote Similarity NPC260491
0.5088 Remote Similarity NPC61506
0.5088 Remote Similarity NPC240476
0.5077 Remote Similarity NPC88964
0.5072 Remote Similarity NPC111786
0.507 Remote Similarity NPC122365
0.507 Remote Similarity NPC602605

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC121886 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
0.7447 Intermediate Similarity NPD1550 Phase 2
0.7447 Intermediate Similarity NPD1552 Clinical (unspecified phase)
0.7059 Intermediate Similarity NPD1934 Phase 0

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