Natural Product: NPC147568

Natural Product IDNPC147568
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
CCFQLQIYEHITNK-SSORVZQWSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 11697907
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 CCFQLQIYEHITNK-SSORVZQWSA-N
Standard InCHI InChI=1S/C30H48O2/c1-19(2)10-9-11-20(3)23-18-26(32)30(8)22-12-13-24-27(4,5)25(31)15-16-28(24,6)21(22)14-17-29(23,30)7/h10,12,14,20,23-26,31-32H,9,11,13,15-18H2,1-8H3/t20-,23-,24+,25+,26+,28-,29-,30-/m1/s1
SMILES CC(=CCC[C@@H](C)[C@H]1C[C@@H]([C@@]2(C)C3=CC[C@H]4C(C)(C)[C@H](CC[C@]4(C)C3=CC[C@]12C)O)O)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   440.37 Volume:   502.881
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Van der Waals volume.
Dense:   0.876 LogP:   5.965
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   4.518
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -5.441
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The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   21.0
TPSA:   40.46
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Topological Polar Surface Area.
H-Bond Acceptor:   2.0
H-Bond Donor:   2.0 Rings:   4.0
Heavy Atoms:   2.0

MedChem Properties

QED Drug-Likeness Score:   0.453 GASA:   1.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   5.009 Fsp3:   0.8
MCE-18:   79.407
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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:   Accepted GSK Rule:   Accepted
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.835 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:   0.046
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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:   0.542 Promiscuous compounds:   0.138

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.863 MDCK Permeability:   -4.677
Pgp-inhibitor:   0.106 Pgp-substrate:   0.565
PAMPA:   0.85
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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):   0.002
20% Bioavailability (F20%):   0.365 30% Bioavailability (F30%):   0.225
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.444 MRP1:   0.549
Plasma Protein Binding (PPB):   91.321% Volume Distribution (VD):   -0.069
Fu: 7.873%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   0.99 BCRP inhibitor:   0.86
BSEP inhibitor:   0.158

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.959
CYP2C19-inhibitor:   0.991 CYP2C19-substrate:   0.637
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.073
CYP2D6-inhibitor:   0.007 CYP2D6-substrate:   0.235
CYP3A4-inhibitor:   0.999 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.999
HLM stability:   0.998
?
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):  14.902 Half-life (T1/2):  0.967

ADMET: Toxicity

hERG Blockers:  0.093 hERG Blockers (10um):  0.389
Human Hepatotoxicity (H-HT):  0.575 Drug-induced Liver Injury (DILI):  0.103
AMES Toxicity:  0.275 Rat Oral Acute Toxicity:  0.361
Maximum Recommended Daily Dose:  0.585 Skin Sensitization:  0.927
Carcinogencity:  0.672 Eye Corrosion:  0.009
Eye Irritation:  0.631 Respiratory Toxicity:  0.794
Drug-induced Neurotoxicity:  0.13 Ototoxicity:  0.667
Hematotoxicity:  0.231 Drug-induced Nephrotoxicity:  0.513
Genotoxicity:  0.09 RPMI-8226 Immunitoxicity:  0.133
A549 Cytotoxicity:  0.342 Hek293 Cytotoxicity:  0.259
BCF:   2.217
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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:   4.513
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.75
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   5.312
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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
NPO41040 Sphaerocoryne gracilis ssp. gracilis Strain Annonaceae Eukaryota n.a. n.a. n.a. PMID[32067457]

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
NPT1794 Individual protein LXR-alpha Homo sapiens EC50 = 30.0 nM PMID[16124770]
NPT1746 Individual protein LXR-beta Homo sapiens EC50 > 50000.0 nM PMID[16124770]
NPT1794 Individual protein LXR-alpha Homo sapiens FC = 8.0 n.a. PMID[16124770]

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 NPC147568 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
0.7857 Intermediate Similarity NPC201852
0.7667 Intermediate Similarity NPC138536
0.7321 Intermediate Similarity NPC205455
0.6393 Remote Similarity NPC202389
0.619 Remote Similarity NPC475772
0.6154 Remote Similarity NPC472942
0.6154 Remote Similarity NPC69622
0.6154 Remote Similarity NPC250575
0.6154 Remote Similarity NPC607637
0.5833 Remote Similarity NPC94393
0.5806 Remote Similarity NPC6707
0.5738 Remote Similarity NPC20853
0.5714 Remote Similarity NPC285702
0.5714 Remote Similarity NPC489791
0.5714 Remote Similarity NPC166745
0.5714 Remote Similarity NPC235464
0.5672 Remote Similarity NPC212948
0.5522 Remote Similarity NPC84271
0.5522 Remote Similarity NPC102414
0.5484 Remote Similarity NPC318136
0.5362 Remote Similarity NPC203035
0.5278 Remote Similarity NPC484797
0.5238 Remote Similarity NPC46160
0.5238 Remote Similarity NPC202642
0.5205 Remote Similarity NPC39082
0.5205 Remote Similarity NPC610107
0.5152 Remote Similarity NPC231310
0.5072 Remote Similarity NPC222845
0.5072 Remote Similarity NPC296577
0.507 Remote Similarity NPC214697

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC147568 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