Natural Product: NPC477915

Natural Product IDNPC477915
Common Name
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The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
20,22-Didehydrotaxisterone
IUPAC Name (2S,3R,5R,10R,13R,14S,17R)-2,3,14-trihydroxy-17-[(E)-6-hydroxy-6-methylhept-2-en-2-yl]-10,13-dimethyl-2,3,4,5,9,11,12,15,16,17-decahydro-1H-cyclopenta[a]phenanthren-6-one
Synonyms 20,22-Didehydrotaxisterone
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 16681644
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0003566] Cholestane steroids
          • [CHEMONTID:0001469] Cholesterols 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 CMIUBJTVLMVMSY-AOTKJMCNSA-N
Standard InCHI InChI=1S/C27H42O5/c1-16(7-6-10-24(2,3)31)17-9-12-27(32)19-13-21(28)20-14-22(29)23(30)15-25(20,4)18(19)8-11-26(17,27)5/h7,13,17-18,20,22-23,29-32H,6,8-12,14-15H2,1-5H3/b16-7+/t17-,18?,20+,22-,23+,25-,26-,27-/m1/s1
SMILES C/C(=C\CCC(C)(C)O)/[C@H]1CC[C@@]2([C@@]1(CCC3C2=CC(=O)[C@H]4[C@@]3(C[C@@H]([C@@H](C4)O)O)C)C)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   446.3 Volume:   477.364
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Van der Waals volume.
Dense:   0.935 LogP:   2.719
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.973
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -4.087
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The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   22.0
TPSA:   97.99
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Topological Polar Surface Area.
H-Bond Acceptor:   5.0
H-Bond Donor:   4.0 Rings:   4.0
Heavy Atoms:   5.0

MedChem Properties

QED Drug-Likeness Score:   0.494 GASA:   1.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   5.013 Fsp3:   0.815
MCE-18:   82.286
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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:   0.353 Fluc inhibitor:   0.003
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.008
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.028
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.324 Promiscuous compounds:   0.357

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -4.795 MDCK Permeability:   -4.619
Pgp-inhibitor:   0.014 Pgp-substrate:   0.273
PAMPA:   0.94
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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):   0.004
20% Bioavailability (F20%):   0.195 30% Bioavailability (F30%):   0.238
50% Bioavailability (F50%):   0.968

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.118 MRP1:   0.634
Plasma Protein Binding (PPB):   84.792% Volume Distribution (VD):   -0.149
Fu: 9.097%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   0.991
OATP1B3 inhibitor:   0.928 BCRP inhibitor:   0.219
BSEP inhibitor:   0.555

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.293 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.001 CYP2D6-substrate:   0.017
CYP3A4-inhibitor:   0.008 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.995
HLM stability:   0.898
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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):  7.42 Half-life (T1/2):  1.87

ADMET: Toxicity

hERG Blockers:  0.051 hERG Blockers (10um):  0.36
Human Hepatotoxicity (H-HT):  0.893 Drug-induced Liver Injury (DILI):  0.014
AMES Toxicity:  0.069 Rat Oral Acute Toxicity:  0.27
Maximum Recommended Daily Dose:  0.93 Skin Sensitization:  0.871
Carcinogencity:  0.859 Eye Corrosion:  0.0
Eye Irritation:  0.105 Respiratory Toxicity:  0.643
Drug-induced Neurotoxicity:  0.036 Ototoxicity:  0.916
Hematotoxicity:  0.138 Drug-induced Nephrotoxicity:  0.757
Genotoxicity:  0.773 RPMI-8226 Immunitoxicity:  0.148
A549 Cytotoxicity:  0.098 Hek293 Cytotoxicity:  0.615
BCF:   0.854
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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:   3.591
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.341
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.338
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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
NPO14761 Serratula wolffii Species Asteraceae Eukaryota roots n.a. n.a. PMID[17417908]
NPO14761 Serratula wolffii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14761 Serratula wolffii Species Asteraceae 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
- Acyrthosiphon pisum LC50 > 100 ppm PMID[17417908]

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 NPC477915 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
0.75 Intermediate Similarity NPC477916
0.7097 Intermediate Similarity NPC204833
0.6935 Remote Similarity NPC150531
0.6825 Remote Similarity NPC302607
0.6719 Remote Similarity NPC50692
0.6719 Remote Similarity NPC260268
0.6719 Remote Similarity NPC152695
0.6719 Remote Similarity NPC319077
0.6719 Remote Similarity NPC76084
0.6719 Remote Similarity NPC97202
0.6719 Remote Similarity NPC601752
0.6562 Remote Similarity NPC209502
0.6462 Remote Similarity NPC149047
0.6462 Remote Similarity NPC214264
0.6462 Remote Similarity NPC475060
0.6462 Remote Similarity NPC85829
0.6462 Remote Similarity NPC48733
0.6462 Remote Similarity NPC171137
0.6462 Remote Similarity NPC83744
0.6364 Remote Similarity NPC296945
0.6364 Remote Similarity NPC220229
0.6364 Remote Similarity NPC601682
0.6324 Remote Similarity NPC317210
0.6176 Remote Similarity NPC202167
0.6176 Remote Similarity NPC49958
0.6129 Remote Similarity NPC603391
0.6087 Remote Similarity NPC476027
0.6 Remote Similarity NPC207251
0.5915 Remote Similarity NPC49492
0.5915 Remote Similarity NPC266728
0.5833 Remote Similarity NPC600136
0.5811 Remote Similarity NPC600372
0.5735 Remote Similarity NPC329417
0.5676 Remote Similarity NPC109973
0.56 Remote Similarity NPC475041
0.5441 Remote Similarity NPC154072
0.527 Remote Similarity NPC326542
0.5143 Remote Similarity NPC11710
0.5143 Remote Similarity NPC600374

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC477915 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