Natural Product: NPC115984

Natural Product IDNPC115984
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 IMNIZYXAQQBADI-JXNJIBEZSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0001445] Bile acids, alcohols and derivatives
          • [CHEMONTID:0002194] Hydroxy bile acids, alcohols and derivatives
            • [CHEMONTID:0000260] Monohydroxy bile acids, alcohols and derivatives

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 IMNIZYXAQQBADI-JXNJIBEZSA-N
Standard InCHI InChI=1S/C25H40O3/c1-16(5-10-23(27)28-4)20-8-9-21-19-7-6-17-15-18(26)11-13-24(17,2)22(19)12-14-25(20,21)3/h6,16,18-22,26H,5,7-15H2,1-4H3/t16-,18-,19-,20-,21-,22+,24-,25+/m0/s1
SMILES C[C@@H](CCC(=O)OC)[C@@H]1CC[C@H]2[C@@H]3CC=C4C[C@H](CC[C@]4(C)[C@@H]3CC[C@]12C)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   388.3 Volume:   427.828
?
Van der Waals volume.
Dense:   0.908 LogP:   4.735
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   4.235
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -5.125
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   5.0 Rigid Bonds:   21.0
TPSA:   46.53
?
Topological Polar Surface Area.
 H-Bond Acceptor:   3.0
H-Bond Donor:   1.0 Rings:   4.0
Heavy Atoms:   3.0

MedChem Properties

QED Drug-Likeness Score:   0.51 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.16 Fsp3:   0.88
MCE-18:   68.596
?
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:   Accepted
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.854 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.009
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.0
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.473 Promiscuous compounds:   0.533

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.988 MDCK Permeability:   -4.915
Pgp-inhibitor:   0.987 Pgp-substrate:   0.171
PAMPA:   0.009
?
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):   0.0
20% Bioavailability (F20%):   0.796 30% Bioavailability (F30%):   0.584
50% Bioavailability (F50%):   0.98

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.019 MRP1:   0.996
Plasma Protein Binding (PPB):   90.652% Volume Distribution (VD):   -0.216
Fu: 9.696%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.982
OATP1B3 inhibitor:   0.826 BCRP inhibitor:   0.521
BSEP inhibitor:   1.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.021 CYP2C19-substrate:   0.018
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.005
CYP3A4-inhibitor:   1.0 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.093
?
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):  10.669 Half-life (T1/2):  0.45

ADMET: Toxicity

hERG Blockers:  0.093 hERG Blockers (10um):  0.261
Human Hepatotoxicity (H-HT):  0.403 Drug-induced Liver Injury (DILI):  0.126
AMES Toxicity:  0.218 Rat Oral Acute Toxicity:  0.211
Maximum Recommended Daily Dose:  0.603 Skin Sensitization:  0.659
Carcinogencity:  0.846 Eye Corrosion:  0.021
Eye Irritation:  0.577 Respiratory Toxicity:  0.494
Drug-induced Neurotoxicity:  0.098 Ototoxicity:  0.548
Hematotoxicity:  0.37 Drug-induced Nephrotoxicity:  0.638
Genotoxicity:  0.047 RPMI-8226 Immunitoxicity:  0.066
A549 Cytotoxicity:  0.067 Hek293 Cytotoxicity:  0.269
BCF:   0.627
?
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:   3.165
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.513
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.99
?
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
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jfca.2005.08.001]
NPO9642 Brassica fruticulosa Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[14518939]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[15286289]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. seed n.a. PMID[20947202]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[24253552]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[8987503]
NPO9642 Brassica fruticulosa Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Wax n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Tissue Culture n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Sprout Seedling n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11043 Pisum sativum Species Fabaceae Eukaryota Seeds n.a. Database[Phenol-Explorer]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11043 Pisum sativum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9642 Brassica fruticulosa Species Brassicaceae 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 NPC115984 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
0.7843 Intermediate Similarity NPC162742
0.7843 Intermediate Similarity NPC304309
0.7843 Intermediate Similarity NPC470228
0.7692 Intermediate Similarity NPC22105
0.7692 Intermediate Similarity NPC34019
0.7692 Intermediate Similarity NPC107059
0.7636 Intermediate Similarity NPC59453
0.7547 Intermediate Similarity NPC136188
0.7547 Intermediate Similarity NPC28657
0.7547 Intermediate Similarity NPC474216
0.7407 Intermediate Similarity NPC230301
0.7407 Intermediate Similarity NPC198968
0.7407 Intermediate Similarity NPC285893
0.7407 Intermediate Similarity NPC134847
0.7321 Intermediate Similarity NPC472265
0.7273 Intermediate Similarity NPC241290
0.7273 Intermediate Similarity NPC164840
0.7273 Intermediate Similarity NPC484739
0.7273 Intermediate Similarity NPC209944
0.7273 Intermediate Similarity NPC155986
0.7193 Intermediate Similarity NPC603646
0.7143 Intermediate Similarity NPC321381
0.7069 Intermediate Similarity NPC473943
0.7037 Intermediate Similarity NPC221758
0.6964 Remote Similarity NPC264245
0.6949 Remote Similarity NPC488870
0.678 Remote Similarity NPC155011
0.6727 Remote Similarity NPC600590
0.6724 Remote Similarity NPC33913
0.6667 Remote Similarity NPC51014
0.6667 Remote Similarity NPC47761
0.6607 Remote Similarity NPC328313
0.6607 Remote Similarity NPC154330
0.6491 Remote Similarity NPC113733
0.623 Remote Similarity NPC243985
0.623 Remote Similarity NPC280710
0.623 Remote Similarity NPC240650
0.6111 Remote Similarity NPC96319
0.6094 Remote Similarity NPC601043
0.6094 Remote Similarity NPC605412
0.6066 Remote Similarity NPC477522
0.6034 Remote Similarity NPC20688
0.6 Remote Similarity NPC328714
0.5902 Remote Similarity NPC318495
0.5873 Remote Similarity NPC474164
0.5862 Remote Similarity NPC151519
0.5738 Remote Similarity NPC87604
0.5692 Remote Similarity NPC474970
0.5667 Remote Similarity NPC76879
0.5645 Remote Similarity NPC1272
0.5645 Remote Similarity NPC470614
0.5556 Remote Similarity NPC474752
0.5556 Remote Similarity NPC474683
0.5484 Remote Similarity NPC31564
0.5484 Remote Similarity NPC145879
0.5397 Remote Similarity NPC153987
0.5312 Remote Similarity NPC474759
0.5312 Remote Similarity NPC44083
0.5286 Remote Similarity NPC309493
0.5238 Remote Similarity NPC26959
0.5167 Remote Similarity NPC81306
0.5156 Remote Similarity NPC474778
0.5156 Remote Similarity NPC474733
0.5147 Remote Similarity NPC176012
0.5147 Remote Similarity NPC599942
0.5075 Remote Similarity NPC475032
0.5072 Remote Similarity NPC5985
0.507 Remote Similarity NPC235126
0.507 Remote Similarity NPC242419

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC115984 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
0.7547 Intermediate Similarity NPD6942 Phase 4
0.7407 Intermediate Similarity NPD7339 Approved
0.7037 Intermediate Similarity NPD4786 Phase 1
0.6111 Remote Similarity NPD3701 Pre-clinical
0.5862 Remote Similarity NPD3667 Phase 4

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