Natural Product: NPC471897

Natural Product IDNPC471897
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
4,(23)-Dihydro-Roburic Acid
IUPAC Name 3-[(1S,2S,4aR,4bS,6aR,9R,10S,10aR,12aR)-1,4a,4b,6a,9,10-hexamethyl-2-propan-2-yl-2,3,4,5,6,7,8,9,10,10a,12,12a-dodecahydrochrysen-1-yl]propanoic acid
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL3289102
PubChem CID 90644336
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 LJWWZZAOSDWGAX-CSHKLQQTSA-N
Standard InCHI InChI=1S/C30H50O2/c1-19(2)22-12-16-30(8)24(28(22,6)15-13-25(31)32)10-9-23-26-21(4)20(3)11-14-27(26,5)17-18-29(23,30)7/h9,19-22,24,26H,10-18H2,1-8H3,(H,31,32)/t20-,21+,22+,24-,26+,27-,28+,29-,30-/m1/s1
SMILES CC1CCC2(CCC3(C(=CCC4C3(CCC(C4(C)CCC(=O)O)C(C)C)C)C2C1C)C)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   442.38 Volume:   505.518
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Van der Waals volume.
Dense:   0.875 LogP:   6.156
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   4.325
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -5.043
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The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   22.0
TPSA:   37.3
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Topological Polar Surface Area.
H-Bond Acceptor:   2.0
H-Bond Donor:   1.0 Rings:   4.0
Heavy Atoms:   2.0

MedChem Properties

QED Drug-Likeness Score:   0.444 GASA:   1.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.754 Fsp3:   0.9
MCE-18:   81.965
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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:   0.518 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:   0.018
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.044
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.471 Promiscuous compounds:   0.006

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.153 MDCK Permeability:   -4.914
Pgp-inhibitor:   0.031 Pgp-substrate:   0.0
PAMPA:   0.041
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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):   0.0
20% Bioavailability (F20%):   0.0 30% Bioavailability (F30%):   0.0
50% Bioavailability (F50%):   0.077

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.946 MRP1:   1.0
Plasma Protein Binding (PPB):   98.119% Volume Distribution (VD):   -0.036
Fu: 2.046%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   0.448
OATP1B3 inhibitor:   0.965 BCRP inhibitor:   0.001
BSEP inhibitor:   0.995

ADMET: Metabolism

CYP1A2-inhibitor:   0.114 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   1.0 CYP2C19-substrate:   0.631
CYP2C9-inhibitor:   1.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.001 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   1.0 CYP3A4-substrate:   0.921
CYP2B6-substrate:   1.0 CYP2C8-inhibitor:   0.998
HLM stability:   0.133
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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):  6.855 Half-life (T1/2):  0.578

ADMET: Toxicity

hERG Blockers:  0.063 hERG Blockers (10um):  0.444
Human Hepatotoxicity (H-HT):  0.431 Drug-induced Liver Injury (DILI):  0.087
AMES Toxicity:  0.018 Rat Oral Acute Toxicity:  0.083
Maximum Recommended Daily Dose:  0.8 Skin Sensitization:  0.024
Carcinogencity:  0.292 Eye Corrosion:  0.002
Eye Irritation:  0.098 Respiratory Toxicity:  0.805
Drug-induced Neurotoxicity:  0.16 Ototoxicity:  0.941
Hematotoxicity:  0.241 Drug-induced Nephrotoxicity:  0.084
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.039
A549 Cytotoxicity:  0.062 Hek293 Cytotoxicity:  0.168
BCF:   1.975
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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:   4.748
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.013
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   5.204
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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
NPO33055 boswellia spp. Species Burseraceae Eukaryota n.a. n.a. n.a. PMID[24844534]

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
NPT324 Individual protein Cyclooxygenase-1 Ovis aries IC50 > 10000.0 nM PMID[18952420]
NPT31 Individual protein Cyclooxygenase-2 Homo sapiens IC50 > 10000.0 nM Open TG-GATES in vivo data: Hematology
NPT956 Individual protein Prostaglandin E synthase Homo sapiens Activity = 92.4 % PMID[17067154]
NPT956 Individual protein Prostaglandin E synthase Homo sapiens IC50 > 10000.0 nM PMID[3236014]

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 NPC471897 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
0.8036 Intermediate Similarity NPC107039
0.7544 Intermediate Similarity NPC471899
0.6885 Remote Similarity NPC471898
0.6316 Remote Similarity NPC469770
0.6094 Remote Similarity NPC280654
0.5909 Remote Similarity NPC86372
0.5846 Remote Similarity NPC231431
0.5735 Remote Similarity NPC184006
0.5672 Remote Similarity NPC260385
0.5672 Remote Similarity NPC110094
0.5645 Remote Similarity NPC82477
0.5484 Remote Similarity NPC27765
0.5484 Remote Similarity NPC122418
0.5484 Remote Similarity NPC491014
0.5385 Remote Similarity NPC290495
0.5147 Remote Similarity NPC610552

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC471897 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