Natural Product: NPC113475

Natural Product IDNPC113475
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 JVMXBCHVJJXDDN-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 5491650
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0002506] Isoflavonoids
        • [CHEMONTID:0001612] Isoflavans
          • [CHEMONTID:0001827] Isoflavanones
            • [CHEMONTID:0003526] 6-prenylated isoflavanones

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 JVMXBCHVJJXDDN-UHFFFAOYSA-N
Standard InCHI InChI=1S/C25H24O6/c1-14(2)8-10-29-15-5-6-16(19(26)11-15)18-13-30-21-12-20-17(7-9-25(3,4)31-20)23(27)22(21)24(18)28/h5-9,11-13,26-27H,10H2,1-4H3
SMILES CC(=CCOc1ccc(c2coc3cc4c(C=CC(C)(C)O4)c(c3c2=O)O)c(c1)O)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   420.16 Volume:   433.107
?
Van der Waals volume.
Dense:   0.97 LogP:   4.771
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.488
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -4.772
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   24.0
TPSA:   89.13
?
Topological Polar Surface Area.
 H-Bond Acceptor:   6.0
H-Bond Donor:   2.0 Rings:   4.0
Heavy Atoms:   6.0

MedChem Properties

QED Drug-Likeness Score:   0.549 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.152 Fsp3:   0.24
MCE-18:   53.677
?
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:   Accepted
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.953 Fluc inhibitor:   0.634
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.75
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.792
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.23 Promiscuous compounds:   0.263

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.998 MDCK Permeability:   -4.677
Pgp-inhibitor:   0.815 Pgp-substrate:   0.006
PAMPA:   0.62
?
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):   0.02
20% Bioavailability (F20%):   0.776 30% Bioavailability (F30%):   0.983
50% Bioavailability (F50%):   0.996

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.078 MRP1:   0.963
Plasma Protein Binding (PPB):   96.06% Volume Distribution (VD):   0.097
Fu: 3.652%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.992
OATP1B3 inhibitor:   0.962 BCRP inhibitor:   0.971
BSEP inhibitor:   0.995

ADMET: Metabolism

CYP1A2-inhibitor:   0.897 CYP1A2-substrate:   0.997
CYP2C19-inhibitor:   0.903 CYP2C19-substrate:   0.874
CYP2C9-inhibitor:   0.996 CYP2C9-substrate:   0.805
CYP2D6-inhibitor:   0.722 CYP2D6-substrate:   0.593
CYP3A4-inhibitor:   0.122 CYP3A4-substrate:   0.971
CYP2B6-substrate:   0.021 CYP2C8-inhibitor:   0.988
HLM stability:   0.925
?
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):  2.065 Half-life (T1/2):  1.497

ADMET: Toxicity

hERG Blockers:  0.207 hERG Blockers (10um):  0.6
Human Hepatotoxicity (H-HT):  0.576 Drug-induced Liver Injury (DILI):  0.794
AMES Toxicity:  0.595 Rat Oral Acute Toxicity:  0.531
Maximum Recommended Daily Dose:  0.689 Skin Sensitization:  0.668
Carcinogencity:  0.733 Eye Corrosion:  0.0
Eye Irritation:  0.686 Respiratory Toxicity:  0.892
Drug-induced Neurotoxicity:  0.161 Ototoxicity:  0.403
Hematotoxicity:  0.216 Drug-induced Nephrotoxicity:  0.433
Genotoxicity:  0.584 RPMI-8226 Immunitoxicity:  0.152
A549 Cytotoxicity:  0.288 Hek293 Cytotoxicity:  0.475
BCF:   1.707
?
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:   4.744
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.239
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.767
?
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
NPO40204 Millettia extensa Species Fabaceae Eukaryota Stems n.a. n.a. PMID[30106294]
NPO40204 Millettia extensa Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[31403786]

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
NPT566 Organism Salmonella typhimurium Salmonella enterica subsp. enterica serovar Typhimurium MIC = 128.0 ug.mL-1 PMID[30106294]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa MIC = 128.0 ug.mL-1 PMID[30106294]

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 NPC113475 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
0.8333 Intermediate Similarity NPC233502
0.7375 Intermediate Similarity NPC484047
0.7067 Intermediate Similarity NPC84124
0.6914 Remote Similarity NPC484041
0.6622 Remote Similarity NPC97716
0.625 Remote Similarity NPC184755
0.6145 Remote Similarity NPC238064
0.6024 Remote Similarity NPC604503
0.6 Remote Similarity NPC184547
0.5976 Remote Similarity NPC484043
0.5802 Remote Similarity NPC231763
0.5714 Remote Similarity NPC229847
0.5641 Remote Similarity NPC203636
0.55 Remote Similarity NPC249824
0.55 Remote Similarity NPC133400
0.5395 Remote Similarity NPC473076
0.5301 Remote Similarity NPC266572
0.5301 Remote Similarity NPC608710
0.5275 Remote Similarity NPC484042
0.5114 Remote Similarity NPC200625
0.5111 Remote Similarity NPC302762
0.5056 Remote Similarity NPC189270
0.5056 Remote Similarity NPC5840

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC113475 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