Natural Product: NPC300147

Natural Product IDNPC300147
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
CAGJKBHKRIWRBO-HLJTUZSJSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 21159133
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001553] Triterpenoids

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 CAGJKBHKRIWRBO-HLJTUZSJSA-N
Standard InCHI InChI=1S/C30H48O4/c1-25(2)14-15-26(3)19(16-25)18-8-9-21-27(4)12-11-22(32)28(5,17-31)20(27)10-13-29(21,6)30(18,7)24(34)23(26)33/h8,19-22,24,31-32,34H,9-17H2,1-7H3/t19-,20+,21+,22-,24-,26-,27-,28-,29+,30-/m0/s1
SMILES CC1(C)CC[C@@]2(C)[C@@H](C1)C1=CC[C@@H]3[C@@]4(C)CC[C@@H]([C@@](C)(CO)[C@@H]4CC[C@@]3(C)[C@]1(C)[C@H](C2=O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   472.36 Volume:   514.542
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Van der Waals volume.
Dense:   0.918 LogP:   3.511
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.557
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -5.251
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The logarithm of aqueous solubility value.
Rotatable Bonds:   1.0 Rigid Bonds:   27.0
TPSA:   77.76
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Topological Polar Surface Area.
H-Bond Acceptor:   4.0
H-Bond Donor:   3.0 Rings:   5.0
Heavy Atoms:   4.0

MedChem Properties

QED Drug-Likeness Score:   0.453 GASA:   0.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   5.056 Fsp3:   0.9
MCE-18:   106.667
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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:   0.726 Fluc inhibitor:   0.0
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.019
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.0
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.393 Promiscuous compounds:   0.251

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.407 MDCK Permeability:   -5.046
Pgp-inhibitor:   0.333 Pgp-substrate:   0.016
PAMPA:   1.0
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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):   0.006
20% Bioavailability (F20%):   0.953 30% Bioavailability (F30%):   0.196
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.963 MRP1:   0.48
Plasma Protein Binding (PPB):   93.347% Volume Distribution (VD):   -0.125
Fu: 5.119%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   0.227 BCRP inhibitor:   0.7
BSEP inhibitor:   0.991

ADMET: Metabolism

CYP1A2-inhibitor:   0.039 CYP1A2-substrate:   0.037
CYP2C19-inhibitor:   0.998 CYP2C19-substrate:   0.031
CYP2C9-inhibitor:   0.354 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.001 CYP2D6-substrate:   0.005
CYP3A4-inhibitor:   0.033 CYP3A4-substrate:   0.085
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.726
HLM stability:   0.941
?
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):  7.276 Half-life (T1/2):  0.851

ADMET: Toxicity

hERG Blockers:  0.033 hERG Blockers (10um):  0.172
Human Hepatotoxicity (H-HT):  0.632 Drug-induced Liver Injury (DILI):  0.412
AMES Toxicity:  0.695 Rat Oral Acute Toxicity:  0.779
Maximum Recommended Daily Dose:  0.509 Skin Sensitization:  0.989
Carcinogencity:  0.965 Eye Corrosion:  0.002
Eye Irritation:  0.326 Respiratory Toxicity:  0.857
Drug-induced Neurotoxicity:  0.225 Ototoxicity:  0.616
Hematotoxicity:  0.823 Drug-induced Nephrotoxicity:  0.913
Genotoxicity:  0.923 RPMI-8226 Immunitoxicity:  0.127
A549 Cytotoxicity:  0.922 Hek293 Cytotoxicity:  0.684
BCF:   1.796
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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:   3.944
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.455
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.768
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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
NPO31315 Pueraria peduncularis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO31315 Pueraria peduncularis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]

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 NPC300147 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
0.6935 Remote Similarity NPC53744
0.6769 Remote Similarity NPC213412
0.6613 Remote Similarity NPC196753
0.6 Remote Similarity NPC480924
0.5692 Remote Similarity NPC474989
0.5672 Remote Similarity NPC230295
0.5672 Remote Similarity NPC98386
0.5441 Remote Similarity NPC238992
0.5441 Remote Similarity NPC470588
0.5385 Remote Similarity NPC290598
0.5385 Remote Similarity NPC30590
0.5373 Remote Similarity NPC101475
0.5294 Remote Similarity NPC235341
0.5294 Remote Similarity NPC253807
0.5294 Remote Similarity NPC158662
0.5278 Remote Similarity NPC270768
0.5278 Remote Similarity NPC59263
0.5278 Remote Similarity NPC210106
0.527 Remote Similarity NPC480919
0.5217 Remote Similarity NPC253402
0.5147 Remote Similarity NPC237344
0.5139 Remote Similarity NPC99254
0.5122 Remote Similarity NPC237503
0.507 Remote Similarity NPC246708
0.5067 Remote Similarity NPC263393
0.5063 Remote Similarity NPC480920

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC300147 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
0.5493 Remote Similarity NPD7645 Phase 2

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