Natural Product: NPC143421

Natural Product IDNPC143421
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
Stoloniferin I
IUPAC Name n.a.
Synonyms Stoloniferin I
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL504970
PubChem CID 44593586
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0000198] Oligosaccharides

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 MKGGCMNXVOUKHJ-QLFFLOGESA-N
Standard InCHI InChI=1S/C56H96O24/c1-11-14-20-23-33-24-21-18-16-15-17-19-22-25-34(57)74-46-42(65)54(79-47-38(61)36(59)29(7)69-55(47)73-33)71-31(9)44(46)78-56-49(76-51(67)27(5)13-3)48(80-52-40(63)37(60)35(58)28(6)68-52)45(32(10)72-56)77-53-41(64)39(62)43(30(8)70-53)75-50(66)26(4)12-2/h26-33,35-49,52-56,58-65H,11-25H2,1-10H3/t26-,27-,28-,29+,30-,31-,32-,33-,35-,36-,37+,38-,39-,40+,41+,42+,43-,44-,45-,46-,47+,48+,49+,52-,53-,54-,55-,56-/m0/s1
SMILES CCCCC[C@H]1CCCCCCCCCC(=O)O[C@H]2[C@H]([C@H](O[C@H]3[C@H](O1)O[C@H](C)[C@@H]([C@@H]3O)O)O[C@@H](C)[C@@H]2O[C@@H]1O[C@@H](C)[C@@H]([C@H]([C@H]1OC(=O)[C@H](CC)C)O[C@@H]1O[C@@H](C)[C@@H]([C@H]([C@H]1O)O)O)O[C@@H]1O[C@@H](C)[C@@H]([C@H]([C@H]1O)O)OC(=O)[C@H](CC)C)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1152.63 Volume:   1128.849
?
Van der Waals volume.
Dense:   1.021 LogP:   3.344
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   3.349
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.864
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   18.0 Rigid Bonds:   49.0
TPSA:   333.04
?
Topological Polar Surface Area.
H-Bond Acceptor:   24.0
H-Bond Donor:   8.0 Rings:   6.0
Heavy Atoms:   24.0

MedChem Properties

QED Drug-Likeness Score:   0.063 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.908 Fsp3:   0.946
MCE-18:   129.468
?
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:   0.991 Fluc inhibitor:   0.333
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.005
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.001
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.548 Promiscuous compounds:   0.04

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.091 MDCK Permeability:   -5.074
Pgp-inhibitor:   0.0 Pgp-substrate:   0.997
PAMPA:   1.0
?
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%):   0.001 30% Bioavailability (F30%):   0.088
50% Bioavailability (F50%):   0.956

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.991
Plasma Protein Binding (PPB):   74.311% Volume Distribution (VD):   -0.26
Fu: 17.559%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   0.993
OATP1B3 inhibitor:   0.997 BCRP inhibitor:   0.0
BSEP inhibitor:   0.137

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:   0.005
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.99
?
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):  0.512 Half-life (T1/2):  3.002

ADMET: Toxicity

hERG Blockers:  0.01 hERG Blockers (10um):  0.15
Human Hepatotoxicity (H-HT):  0.281 Drug-induced Liver Injury (DILI):  0.966
AMES Toxicity:  0.631 Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.0 Skin Sensitization:  1.0
Carcinogencity:  0.0 Eye Corrosion:  0.0
Eye Irritation:  0.002 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  0.999
Hematotoxicity:  0.691 Drug-induced Nephrotoxicity:  0.942
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.681
A549 Cytotoxicity:  0.911 Hek293 Cytotoxicity:  0.18
BCF:   0.739
?
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:   3.41
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.195
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.225
?
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
NPO2520 Ipomoea murucoides Species Convolvulaceae Eukaryota Roots Ixpantepec, in the state of Oaxaca, Mexico 1996-DEC PMID[16124750]
NPO2520 Ipomoea murucoides Species Convolvulaceae Eukaryota flowers n.a. n.a. PMID[16643033]
NPO2520 Ipomoea murucoides Species Convolvulaceae Eukaryota n.a. n.a. n.a. PMID[18500841]
NPO2520 Ipomoea murucoides Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]

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
NPT91 Cell line KB Homo sapiens ED50 > 20.0 ug ml-1 PMID[19506060]
NPT1171 Cell line HEp-2 Homo sapiens ED50 > 20.0 ug ml-1 DOI[10.6019/CHEMBL1201861]
NPT165 Cell line HeLa Homo sapiens ED50 > 20.0 ug ml-1 PMID[22765894]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC > 512.0 ug.mL-1 DrugMatrix in vitro pharmacology data
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 512.0 ug.mL-1 DrugMatrix in vitro pharmacology data
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 256.0 ug.mL-1 PMID[19506060]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 64.0 ug.mL-1 PMID[22115593]

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 NPC143421 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
0.9867 High Similarity NPC477319
0.974 High Similarity NPC290012
0.9737 High Similarity NPC307400
0.9737 High Similarity NPC27289
0.925 High Similarity NPC123204
0.9125 High Similarity NPC126685
0.8974 High Similarity NPC267592
0.8889 High Similarity NPC183888
0.8889 High Similarity NPC259294
0.8816 High Similarity NPC113745
0.8816 High Similarity NPC477320
0.8816 High Similarity NPC477323
0.8816 High Similarity NPC477325
0.8816 High Similarity NPC609436
0.875 High Similarity NPC472204
0.8293 Intermediate Similarity NPC119583
0.8289 Intermediate Similarity NPC146380
0.8193 Intermediate Similarity NPC483170
0.8095 Intermediate Similarity NPC115013
0.8025 Intermediate Similarity NPC477326
0.7778 Intermediate Similarity NPC604005
0.7778 Intermediate Similarity NPC605014
0.7683 Intermediate Similarity NPC478734
0.7683 Intermediate Similarity NPC89843
0.7586 Intermediate Similarity NPC184915
0.7586 Intermediate Similarity NPC224953
0.7527 Intermediate Similarity NPC63404
0.75 Intermediate Similarity NPC478733
0.7471 Intermediate Similarity NPC477317
0.7471 Intermediate Similarity NPC477318
0.7439 Intermediate Similarity NPC22742
0.7439 Intermediate Similarity NPC477346
0.7416 Intermediate Similarity NPC44782
0.7407 Intermediate Similarity NPC281563
0.7396 Intermediate Similarity NPC10121
0.7396 Intermediate Similarity NPC198918
0.7381 Intermediate Similarity NPC477344
0.734 Intermediate Similarity NPC35338
0.734 Intermediate Similarity NPC204214
0.734 Intermediate Similarity NPC92283
0.7326 Intermediate Similarity NPC297768
0.7326 Intermediate Similarity NPC472205
0.7273 Intermediate Similarity NPC169345
0.7209 Intermediate Similarity NPC146992
0.7209 Intermediate Similarity NPC85759
0.7159 Intermediate Similarity NPC476087
0.7159 Intermediate Similarity NPC475667
0.7079 Intermediate Similarity NPC478732
0.7045 Intermediate Similarity NPC294748
0.7 Intermediate Similarity NPC475270
0.7 Intermediate Similarity NPC475327
0.7 Intermediate Similarity NPC606819
0.6977 Remote Similarity NPC600446
0.6977 Remote Similarity NPC605013
0.6966 Remote Similarity NPC238264
0.6966 Remote Similarity NPC477345
0.6932 Remote Similarity NPC173328
0.6889 Remote Similarity NPC238056
0.6875 Remote Similarity NPC124878
0.6875 Remote Similarity NPC231888
0.6782 Remote Similarity NPC158302
0.6739 Remote Similarity NPC472200
0.6705 Remote Similarity NPC109887
0.6667 Remote Similarity NPC186992
0.6596 Remote Similarity NPC475164
0.6562 Remote Similarity NPC475241
0.6535 Remote Similarity NPC10883
0.6484 Remote Similarity NPC478730
0.6429 Remote Similarity NPC477350
0.6354 Remote Similarity NPC473605
0.6354 Remote Similarity NPC475375
0.6321 Remote Similarity NPC472352
0.6292 Remote Similarity NPC477331
0.625 Remote Similarity NPC147032
0.617 Remote Similarity NPC478731
0.6146 Remote Similarity NPC269318
0.6067 Remote Similarity NPC477349
0.6042 Remote Similarity NPC475525
0.6042 Remote Similarity NPC475540
0.5979 Remote Similarity NPC476066
0.5905 Remote Similarity NPC290276
0.5905 Remote Similarity NPC611287
0.5888 Remote Similarity NPC600721
0.5888 Remote Similarity NPC605872
0.5876 Remote Similarity NPC163409
0.578 Remote Similarity NPC600940
0.5766 Remote Similarity NPC471024
0.5701 Remote Similarity NPC600672
0.5699 Remote Similarity NPC479059
0.5667 Remote Similarity NPC477329
0.5632 Remote Similarity NPC478729
0.5619 Remote Similarity NPC77651
0.5591 Remote Similarity NPC477332
0.5579 Remote Similarity NPC479061
0.5579 Remote Similarity NPC60849
0.5567 Remote Similarity NPC478726
0.5556 Remote Similarity NPC477330
0.5556 Remote Similarity NPC610996
0.5521 Remote Similarity NPC479058
0.5521 Remote Similarity NPC479060
0.5472 Remote Similarity NPC28069
0.5385 Remote Similarity NPC477328
0.5364 Remote Similarity NPC471025
0.5357 Remote Similarity NPC610997
0.5354 Remote Similarity NPC162925
0.5294 Remote Similarity NPC478728
0.5258 Remote Similarity NPC478722
0.5243 Remote Similarity NPC478727
0.5204 Remote Similarity NPC44682
0.5204 Remote Similarity NPC478724
0.5109 Remote Similarity NPC475425
0.5102 Remote Similarity NPC478725
0.5051 Remote Similarity NPC478723
0.5049 Remote Similarity NPC477347

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC143421 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