Natural Product: NPC215311

Natural Product IDNPC215311
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 Neobavaisoflavone
IUPAC Name 7-hydroxy-3-[4-hydroxy-3-(3-methylbut-2-enyl)phenyl]chromen-4-one
Synonyms Neobavaisoflavone
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL512693
PubChem CID 5320053
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0002506] Isoflavonoids
        • [CHEMONTID:0002901] Isoflav-2-enes
          • [CHEMONTID:0000494] Isoflavones

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 OBGPEBYHGIUFBN-UHFFFAOYSA-N
Standard InCHI InChI=1S/C20H18O4/c1-12(2)3-4-14-9-13(5-8-18(14)22)17-11-24-19-10-15(21)6-7-16(19)20(17)23/h3,5-11,21-22H,4H2,1-2H3
SMILES CC(=CCc1cc(ccc1O)c1coc2cc(ccc2c1=O)O)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   322.12 Volume:   340.24
?
Van der Waals volume.
Dense:   0.947 LogP:   3.432
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.146
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.559
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   3.0 Rigid Bonds:   19.0
TPSA:   70.67
?
Topological Polar Surface Area.
 H-Bond Acceptor:   4.0
H-Bond Donor:   2.0 Rings:   3.0
Heavy Atoms:   4.0

MedChem Properties

QED Drug-Likeness Score:   0.702 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.519 Fsp3:   0.15
MCE-18:   18.0
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Accepted GSK Rule:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.879 Fluc inhibitor:   0.977
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.976
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.519
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.463 Promiscuous compounds:   0.048

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.699 MDCK Permeability:   -4.685
Pgp-inhibitor:   0.014 Pgp-substrate:   0.136
PAMPA:   0.811
?
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):   0.24
20% Bioavailability (F20%):   0.999 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.312
Plasma Protein Binding (PPB):   93.217% Volume Distribution (VD):   0.142
Fu: 6.34%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.314
OATP1B3 inhibitor:   0.866 BCRP inhibitor:   0.991
BSEP inhibitor:   0.314

ADMET: Metabolism

CYP1A2-inhibitor:   0.349 CYP1A2-substrate:   1.0
CYP2C19-inhibitor:   0.792 CYP2C19-substrate:   1.0
CYP2C9-inhibitor:   0.35 CYP2C9-substrate:   0.995
CYP2D6-inhibitor:   0.994 CYP2D6-substrate:   0.292
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.016 CYP2C8-inhibitor:   1.0
HLM stability:   0.999
?
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):  8.347 Half-life (T1/2):  1.116

ADMET: Toxicity

hERG Blockers:  0.166 hERG Blockers (10um):  0.604
Human Hepatotoxicity (H-HT):  0.586 Drug-induced Liver Injury (DILI):  0.732
AMES Toxicity:  0.674 Rat Oral Acute Toxicity:  0.768
Maximum Recommended Daily Dose:  0.797 Skin Sensitization:  0.732
Carcinogencity:  0.681 Eye Corrosion:  0.004
Eye Irritation:  0.931 Respiratory Toxicity:  0.892
Drug-induced Neurotoxicity:  0.545 Ototoxicity:  0.38
Hematotoxicity:  0.148 Drug-induced Nephrotoxicity:  0.448
Genotoxicity:  0.966 RPMI-8226 Immunitoxicity:  0.073
A549 Cytotoxicity:  0.388 Hek293 Cytotoxicity:  0.692
BCF:   1.682
?
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:   4.716
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.671
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.31
?
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
NPO24314 Erythrina sigmoidea Species Fabaceae Eukaryota n.a. bark n.a. PMID[14994185]
NPO6673 Erythrina latissima Species Fabaceae Eukaryota n.a. stem wood n.a. PMID[15649516]
NPO30150 Psoralea corylifolia Species Fabaceae Eukaryota seeds n.a. n.a. PMID[18359631]
NPO11451 Lespedeza cyrtobotrya Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[19102656]
NPO28809 Cullen corylifolium Species Fabaceae Eukaryota n.a. fruit n.a. PMID[20663508]
NPO28809 Cullen corylifolium Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[24507928]
NPO30150 Psoralea corylifolia Species Fabaceae Eukaryota Fruits n.a. n.a. PMID[25710081]
NPO30150 Psoralea corylifolia Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[3069958]
NPO24314 Erythrina sigmoidea Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[7964799]
NPO30150 Psoralea corylifolia Species Fabaceae Eukaryota n.a. seed n.a. PMID[8759164]
NPO28809 Cullen corylifolium Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[9544566]
NPO11451 Lespedeza cyrtobotrya Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24314 Erythrina sigmoidea Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1470 Fructus psoraleae corylifoliae n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO6673 Erythrina latissima Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28809 Cullen corylifolium Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO10080 Teucrium betonicum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO30150 Psoralea corylifolia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6673 Erythrina latissima Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11451 Lespedeza cyrtobotrya Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24314 Erythrina sigmoidea Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30150 Psoralea corylifolia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11451 Lespedeza cyrtobotrya Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28809 Cullen corylifolium Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24314 Erythrina sigmoidea Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6673 Erythrina latissima Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1470 Fructus psoraleae corylifoliae n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO30150 Psoralea corylifolia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28809 Cullen corylifolium Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO24314 Erythrina sigmoidea Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28809 Cullen corylifolium Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10080 Teucrium betonicum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11451 Lespedeza cyrtobotrya Species Fabaceae 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
NPT20556 Single protein Replicase polyprotein 1ab Severe acute respiratory syndrome coronavirus 2 Inhibition = 84.9 % PMID[36651644]
NPT20556 Single protein Replicase polyprotein 1ab Severe acute respiratory syndrome coronavirus 2 Inhibition = 18.0 % PMID[36651644]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT111 Cell line K562 Homo sapiens IC50 > 10000.0 nM PMID[25710081]
NPT81 Cell line A549 Homo sapiens IC50 > 10000.0 nM PMID[25710081]
NPT566 Organism Salmonella typhimurium Salmonella enterica subsp. enterica serovar Typhimurium Inhibition > 90.0 % PMID[3069957]
NPT566 Organism Salmonella typhimurium Salmonella enterica subsp. enterica serovar Typhimurium Inhibition = 97.0 % PMID[3069957]
NPT566 Organism Salmonella typhimurium Salmonella enterica subsp. enterica serovar Typhimurium Inhibition = 67.0 % PMID[3069957]
NPT566 Organism Salmonella typhimurium Salmonella enterica subsp. enterica serovar Typhimurium Inhibition = 98.0 % PMID[3069957]
NPT566 Organism Salmonella typhimurium Salmonella enterica subsp. enterica serovar Typhimurium Inhibition = 96.0 % PMID[3069957]
NPT566 Organism Salmonella typhimurium Salmonella enterica subsp. enterica serovar Typhimurium Inhibition = 72.0 % PMID[3069957]
NPT566 Organism Salmonella typhimurium Salmonella enterica subsp. enterica serovar Typhimurium Inhibition = 2.0 % PMID[3069957]
NPT566 Organism Salmonella typhimurium Salmonella enterica subsp. enterica serovar Typhimurium Inhibition = 74.0 % PMID[3069957]
NPT566 Organism Salmonella typhimurium Salmonella enterica subsp. enterica serovar Typhimurium Inhibition = 17.0 % PMID[3069957]
NPT566 Organism Salmonella typhimurium Salmonella enterica subsp. enterica serovar Typhimurium Inhibition = 66.0 % PMID[3069957]
NPT566 Organism Salmonella typhimurium Salmonella enterica subsp. enterica serovar Typhimurium Inhibition = 53.0 % PMID[3069957]
NPT566 Organism Salmonella typhimurium Salmonella enterica subsp. enterica serovar Typhimurium Inhibition = 15.0 % PMID[3069957]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 62400.0 nM PMID[8759164]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 7800.0 nM PMID[8759164]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 2500.0 nM PMID[8759164]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 3.2 ug.mL-1 PMID[7964799]
NPT87 Organism Aspergillus fumigatus Aspergillus fumigatus MIC = 50.0 ug.mL-1 PMID[7964799]
NPT85 Organism Filobasidiella neoformans Cryptococcus neoformans MIC = 50.0 ug.mL-1 PMID[7964799]
NPT20972 Cell line SU.86.86 Homo sapiens Activity > 20.0 % PMID[31980363]
NPT2 Others Unspecified n.a. IC50 = 9400.0 nM PMID[19102656]
NPT2 Others Unspecified n.a. IC50 = 284100.0 nM PMID[25710081]

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 NPC215311 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
0.8308 Intermediate Similarity NPC123653
0.746 Intermediate Similarity NPC213659
0.746 Intermediate Similarity NPC326109
0.7188 Intermediate Similarity NPC172250
0.7031 Intermediate Similarity NPC161124
0.7015 Intermediate Similarity NPC149875
0.6818 Remote Similarity NPC48624
0.6379 Remote Similarity NPC234560
0.6167 Remote Similarity NPC242893
0.6087 Remote Similarity NPC80962
0.6029 Remote Similarity NPC261227
0.5875 Remote Similarity NPC324447
0.5811 Remote Similarity NPC7989
0.5775 Remote Similarity NPC475705
0.5753 Remote Similarity NPC104555
0.5738 Remote Similarity NPC212767
0.5692 Remote Similarity NPC209560
0.5692 Remote Similarity NPC490700
0.5676 Remote Similarity NPC104406
0.5672 Remote Similarity NPC139364
0.5625 Remote Similarity NPC487215
0.56 Remote Similarity NPC223701
0.56 Remote Similarity NPC472583
0.5571 Remote Similarity NPC238279
0.5522 Remote Similarity NPC12377
0.5507 Remote Similarity NPC259166
0.5467 Remote Similarity NPC285623
0.5455 Remote Similarity NPC203747
0.5455 Remote Similarity NPC609386
0.5441 Remote Similarity NPC80710
0.5312 Remote Similarity NPC235428
0.5286 Remote Similarity NPC35544
0.5278 Remote Similarity NPC203077
0.5278 Remote Similarity NPC232947
0.527 Remote Similarity NPC166036
0.5263 Remote Similarity NPC108859
0.5217 Remote Similarity NPC191741
0.5211 Remote Similarity NPC20472
0.52 Remote Similarity NPC266572
0.5135 Remote Similarity NPC233918
0.5135 Remote Similarity NPC611071
0.5072 Remote Similarity NPC262623
0.5068 Remote Similarity NPC607759

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC215311 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