Natural Product: NPC103167

Natural Product IDNPC103167
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 SQBVRNCDBATODN-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 12309400
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0002506] Isoflavonoids
        • [CHEMONTID:0003530] Pyranoisoflavonoids

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 SQBVRNCDBATODN-UHFFFAOYSA-N
Standard InCHI InChI=1S/C22H18O6/c1-22(2)7-6-13-20-14(9-18(24-3)21(13)28-22)19(23)15(10-25-20)12-4-5-16-17(8-12)27-11-26-16/h4-10H,11H2,1-3H3
SMILES CC1(C)C=Cc2c3c(cc(c2O1)OC)c(=O)c(co3)c1ccc2c(c1)OCO2

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   378.11 Volume:   375.299
?
Van der Waals volume.
Dense:   1.007 LogP:   3.694
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.348
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -5.325
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   2.0 Rigid Bonds:   27.0
TPSA:   67.13
?
Topological Polar Surface Area.
 H-Bond Acceptor:   6.0
H-Bond Donor:   0.0 Rings:   5.0
Heavy Atoms:   6.0

MedChem Properties

QED Drug-Likeness Score:   0.659 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   2.872 Fsp3:   0.227
MCE-18:   60.148
?
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:   0.693 Fluc inhibitor:   0.576
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.909
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.477
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.257 Promiscuous compounds:   0.179

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.746 MDCK Permeability:   -4.713
Pgp-inhibitor:   0.94 Pgp-substrate:   0.006
PAMPA:   0.224
?
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):   0.001
20% Bioavailability (F20%):   0.105 30% Bioavailability (F30%):   0.007
50% Bioavailability (F50%):   0.854

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.61 MRP1:   0.769
Plasma Protein Binding (PPB):   96.574% Volume Distribution (VD):   0.051
Fu: 3.037%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.995
OATP1B3 inhibitor:   0.989 BCRP inhibitor:   0.392
BSEP inhibitor:   1.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.961 CYP1A2-substrate:   1.0
CYP2C19-inhibitor:   0.81 CYP2C19-substrate:   0.799
CYP2C9-inhibitor:   0.813 CYP2C9-substrate:   0.803
CYP2D6-inhibitor:   0.761 CYP2D6-substrate:   1.0
CYP3A4-inhibitor:   0.014 CYP3A4-substrate:   0.999
CYP2B6-substrate:   0.372 CYP2C8-inhibitor:   0.111
HLM stability:   0.255
?
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):  3.745 Half-life (T1/2):  0.78

ADMET: Toxicity

hERG Blockers:  0.234 hERG Blockers (10um):  0.549
Human Hepatotoxicity (H-HT):  0.648 Drug-induced Liver Injury (DILI):  0.921
AMES Toxicity:  0.664 Rat Oral Acute Toxicity:  0.652
Maximum Recommended Daily Dose:  0.818 Skin Sensitization:  0.253
Carcinogencity:  0.923 Eye Corrosion:  0.005
Eye Irritation:  0.741 Respiratory Toxicity:  0.665
Drug-induced Neurotoxicity:  0.605 Ototoxicity:  0.362
Hematotoxicity:  0.523 Drug-induced Nephrotoxicity:  0.53
Genotoxicity:  0.782 RPMI-8226 Immunitoxicity:  0.182
A549 Cytotoxicity:  0.14 Hek293 Cytotoxicity:  0.463
BCF:   1.939
?
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:   4.489
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.811
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   5.875
?
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
NPO29483 Swartzia schomburgkii Species Fabaceae Eukaryota n.a. suriname rainforest n.a. PMID[11087583]
NPO28682 Jatropha multifida Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[19036584]
NPO28682 Jatropha multifida Species Euphorbiaceae Eukaryota stems Botanical Garden, Osmania University, Hyderabad, Andhra Pradesh 2006-AUG PMID[21534583]
NPO28626 Isodon rubescens Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[25590529]
NPO29252 Moneses uniflora Species Ericaceae Eukaryota n.a. n.a. n.a. PMID[8984155]
NPO29132 Agaricus campestris Species Agaricaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28626 Isodon rubescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29288 Diplorhynchus condylocarpon Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28682 Jatropha multifida Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28728 Scutellaria planipes Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29339 Didemnum moseleyi Species Didemnidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29022 Sarcococca wallichii Species Buxaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28711 Artabotrys hexapetalus Species Annonaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28606 Lemaireocereus thurberi Species Cactaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29252 Moneses uniflora Species Ericaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO28711 Artabotrys hexapetalus Species Annonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29132 Agaricus campestris Species Agaricaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28626 Isodon rubescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28711 Artabotrys hexapetalus Species Annonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29132 Agaricus campestris Species Agaricaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29132 Agaricus campestris Species Agaricaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28711 Artabotrys hexapetalus Species Annonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28626 Isodon rubescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28728 Scutellaria planipes Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28664 Hydrangea arborescens Species Hydrangeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29252 Moneses uniflora Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29164 Lophostemon confertus Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28626 Isodon rubescens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29483 Swartzia schomburgkii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29288 Diplorhynchus condylocarpon Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29339 Didemnum moseleyi Species Didemnidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29269 Celsia roripifolia Species Scrophulariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28682 Jatropha multifida Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28699 Vincetoxicum nigrum Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28798 Calophyllum macrocarpum Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29022 Sarcococca wallichii Species Buxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28711 Artabotrys hexapetalus Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29393 Hapalopilus rutilans Species Phanerochaetaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29132 Agaricus campestris Species Agaricaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28910 Dacus cucumis Species Tephritidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28767 Siparuna apiosyce Species Siparunaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28606 Lemaireocereus thurberi Species Cactaceae 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 NPC103167 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
0.7826 Intermediate Similarity NPC18284
0.7761 Intermediate Similarity NPC113055
0.6286 Remote Similarity NPC607923
0.6267 Remote Similarity NPC273021
0.6029 Remote Similarity NPC148497
0.5733 Remote Similarity NPC128961
0.5634 Remote Similarity NPC602183
0.5541 Remote Similarity NPC600644
0.5385 Remote Similarity NPC608710
0.5333 Remote Similarity NPC260640
0.5316 Remote Similarity NPC302741
0.5316 Remote Similarity NPC144162
0.5205 Remote Similarity NPC602689
0.5132 Remote Similarity NPC472408
0.5119 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 NPC103167 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