Natural Product: NPC536075

Natural Product IDNPC536075
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
Solaradixine
IUPAC Name (2~{S},3~{R},4~{R},5~{R},6~{S})-2-[(2~{R},3~{R},4~{S},5~{S},6~{R})-4-[(2~{S},3~{R},4~{S},5~{S},6~{R})-4,5-dihydroxy-6-(hydroxymethyl)-3-[(2~{S},3~{R},4~{S},5~{S},6~{R})-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydropyran-2-yl]oxy-tetrahydropyran-2-yl]oxy-5-hydroxy-6-(hydroxymethyl)-2-[(5'~{R},6~{R},7~{S},9~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-piperidine]-16-yl]oxy-tetrahydropyran-3-yl]oxy-6-methyl-tetrahydropyran-3,4,5-triol
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]

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 GIHGNUCHPKDXJW-FGSZFCSWSA-N
Standard InCHI InChI=1S/C51H83NO21/c1-20-8-13-51(52-16-20)21(2)32-28(73-51)15-27-25-7-6-23-14-24(9-11-49(23,4)26(25)10-12-50(27,32)5)66-48-44(72-45-40(63)37(60)33(56)22(3)65-45)42(36(59)31(19-55)69-48)70-47-43(39(62)35(58)30(18-54)68-47)71-46-41(64)38(61)34(57)29(17-53)67-46/h6,20-22,24-48,52-64H,7-19H2,1-5H3/t20-,21+,22+,24+,25?,26?,27?,28?,29-,30-,31-,32?,33+,34-,35-,36+,37-,38+,39+,40-,41-,42+,43-,44-,45+,46+,47+,48-,49+,50+,51-/m1/s1
SMILES C[C@@H]1CC[C@@]2(NC1)OC1CC3C4CC=C5C[C@@H](O[C@@H]6O[C@H](CO)[C@H](O)[C@H](O[C@@H]7O[C@H](CO)[C@@H](O)[C@H](O)[C@H]7O[C@@H]7O[C@H](CO)[C@@H](O)[C@H](O)[C@H]7O)[C@H]6O[C@@H]6O[C@@H](C)[C@H](O)[C@@H](O)[C@H]6O)CC[C@]5(C)C4CC[C@]3(C)C1[C@@H]2C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1045.55 Volume:   998.042
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Van der Waals volume.
Dense:   1.048 LogP:   0.297
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.257
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.672
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The logarithm of aqueous solubility value.
Rotatable Bonds:   11.0 Rigid Bonds:   54.0
TPSA:   337.86
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Topological Polar Surface Area.
H-Bond Acceptor:   22.0
H-Bond Donor:   13.0 Rings:   10.0
Heavy Atoms:   22.0

MedChem Properties

QED Drug-Likeness Score:   0.096 GASA:   1.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.231 Fsp3:   0.961
MCE-18:   259.76
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MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
Lipinski Rule-of-5:   Accepted
Pfizer Rule:   Rejected GSK Rule:   Accepted
Golden Triangle Rule:   Accepted BMS Rule:   1
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.613 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:   0.004
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.062
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.025 Promiscuous compounds:   0.005

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.49 MDCK Permeability:   -5.188
Pgp-inhibitor:   0.0 Pgp-substrate:   0.737
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):   0.0
20% Bioavailability (F20%):   0.031 30% Bioavailability (F30%):   0.932
50% Bioavailability (F50%):   0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.048 MRP1:   0.608
Plasma Protein Binding (PPB):   54.094% Volume Distribution (VD):   -0.391
Fu: 34.582%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   0.999 BCRP inhibitor:   0.0
BSEP inhibitor:   0.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.002 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.002
HLM stability:   0.0
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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):  -0.188 Half-life (T1/2):  3.273

ADMET: Toxicity

hERG Blockers:  0.008 hERG Blockers (10um):  0.011
Human Hepatotoxicity (H-HT):  0.624 Drug-induced Liver Injury (DILI):  0.924
AMES Toxicity:  0.989 Rat Oral Acute Toxicity:  0.001
Maximum Recommended Daily Dose:  0.002 Skin Sensitization:  1.0
Carcinogencity:  0.023 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.224 Drug-induced Nephrotoxicity:  0.821
Genotoxicity:  0.012 RPMI-8226 Immunitoxicity:  0.4
A549 Cytotoxicity:  0.986 Hek293 Cytotoxicity:  0.868
BCF:   1.424
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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:   3.401
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.581
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   3.742
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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
NPO14085 Solanum laciniatum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO14085 Solanum laciniatum Species Solanaceae 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 NPC536075 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
0.9271 High Similarity NPC150057
0.9271 High Similarity NPC147753
0.7941 Intermediate Similarity NPC122819
0.7353 Intermediate Similarity NPC15249
0.7353 Intermediate Similarity NPC25455
0.7168 Intermediate Similarity NPC287885
0.6607 Remote Similarity NPC102016
0.6607 Remote Similarity NPC95051
0.6429 Remote Similarity NPC300557
0.6325 Remote Similarity NPC218571
0.6325 Remote Similarity NPC487615
0.6306 Remote Similarity NPC98696
0.625 Remote Similarity NPC602423
0.6154 Remote Similarity NPC309278
0.6126 Remote Similarity NPC305423
0.6126 Remote Similarity NPC113044
0.6126 Remote Similarity NPC283829
0.6126 Remote Similarity NPC161676
0.5946 Remote Similarity NPC94272
0.5763 Remote Similarity NPC73243
0.5763 Remote Similarity NPC244086
0.5763 Remote Similarity NPC84956
0.5726 Remote Similarity NPC48886
0.5726 Remote Similarity NPC94881
0.5691 Remote Similarity NPC480553
0.5678 Remote Similarity NPC480555
0.5678 Remote Similarity NPC150372
0.5667 Remote Similarity NPC247037
0.5641 Remote Similarity NPC477809
0.5546 Remote Similarity NPC475182
0.5545 Remote Similarity NPC485606
0.5528 Remote Similarity NPC249265
0.5528 Remote Similarity NPC480554
0.5487 Remote Similarity NPC600456
0.5484 Remote Similarity NPC23808
0.5484 Remote Similarity NPC87998
0.5447 Remote Similarity NPC194207
0.5447 Remote Similarity NPC22779
0.544 Remote Similarity NPC477811
0.5431 Remote Similarity NPC470748
0.5431 Remote Similarity NPC600116
0.5424 Remote Similarity NPC470433
0.5424 Remote Similarity NPC46190
0.5424 Remote Similarity NPC171073
0.5385 Remote Similarity NPC477808
0.5378 Remote Similarity NPC248746
0.5366 Remote Similarity NPC13193
0.5347 Remote Similarity NPC147835
0.5347 Remote Similarity NPC253645
0.5347 Remote Similarity NPC85001
0.5347 Remote Similarity NPC95920
0.5339 Remote Similarity NPC486388
0.5333 Remote Similarity NPC42171
0.5299 Remote Similarity NPC14704
0.5259 Remote Similarity NPC306991
0.5234 Remote Similarity NPC232054
0.5231 Remote Similarity NPC480556
0.5229 Remote Similarity NPC296686
0.521 Remote Similarity NPC40440
0.5207 Remote Similarity NPC6806
0.5182 Remote Similarity NPC165439
0.5172 Remote Similarity NPC295980
0.5161 Remote Similarity NPC269297
0.5161 Remote Similarity NPC222202
0.5156 Remote Similarity NPC308140
0.512 Remote Similarity NPC475333
0.512 Remote Similarity NPC224098
0.512 Remote Similarity NPC208383
0.5085 Remote Similarity NPC141433
0.504 Remote Similarity NPC486386

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC536075 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
0.9271 High Similarity NPD8450 Suspended
0.7941 Intermediate Similarity NPD8449 Approved

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