Natural Product: NPC307400

Natural Product IDNPC307400
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
Stoloniferin Iii
IUPAC Name n.a.
Synonyms stoloniferin III
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL447968
PubChem CID 44575416
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 VQJSKLDVGOAPNT-XNPMHXEPSA-N
Standard InCHI InChI=1S/C61H106O24/c1-10-13-15-16-18-22-27-31-40(63)80-55-54(85-57-46(69)43(66)41(64)33(5)73-57)51(82-58-47(70)45(68)49(35(7)75-58)81-56(72)32(4)12-3)37(9)77-61(55)83-50-36(8)76-59-48(71)52(50)79-39(62)30-26-23-20-17-19-21-25-29-38(28-24-14-11-2)78-60-53(84-59)44(67)42(65)34(6)74-60/h32-38,41-55,57-61,64-71H,10-31H2,1-9H3/t32-,33-,34+,35-,36-,37-,38-,41-,42-,43+,44-,45-,46+,47+,48+,49-,50-,51-,52-,53+,54+,55+,57-,58-,59-,60-,61-/m0/s1
SMILES CCCCCCCCCC(=O)O[C@H]1[C@H](O[C@H]2[C@H](C)O[C@@H]3[C@@H]([C@@H]2OC(=O)CCCCCCCCC[C@@H](O[C@H]2[C@H](O3)[C@@H](O)[C@H]([C@H](O2)C)O)CCCCC)O)O[C@H]([C@@H]([C@H]1O[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)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1222.71 Volume:   1215.329
?
Van der Waals volume.
Dense:   1.006 LogP:   4.685
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   4.308
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -4.289
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   24.0 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:   0.042 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.99 Fsp3:   0.951
MCE-18:   124.235
?
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:   0.998 Fluc inhibitor:   0.333
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.004
?
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:   0.542 Promiscuous compounds:   0.062

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.626 MDCK Permeability:   -5.032
Pgp-inhibitor:   0.0 Pgp-substrate:   0.996
PAMPA:   0.999
?
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):   0.078
20% Bioavailability (F20%):   0.064 30% Bioavailability (F30%):   0.621
50% Bioavailability (F50%):   0.992

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.997
Plasma Protein Binding (PPB):   93.14% Volume Distribution (VD):   -0.062
Fu: 5.359%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   0.823
OATP1B3 inhibitor:   0.998 BCRP inhibitor:   0.0
BSEP inhibitor:   0.086

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:   0.154
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   1.0
HLM stability:   0.985
?
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):  0.674 Half-life (T1/2):  2.891

ADMET: Toxicity

hERG Blockers:  0.031 hERG Blockers (10um):  0.217
Human Hepatotoxicity (H-HT):  0.388 Drug-induced Liver Injury (DILI):  0.985
AMES Toxicity:  0.598 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:  0.005 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  0.999
Hematotoxicity:  0.756 Drug-induced Nephrotoxicity:  0.964
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.748
A549 Cytotoxicity:  0.998 Hek293 Cytotoxicity:  0.41
BCF:   0.653
?
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:   4.357
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.969
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.754
?
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
NPO23352 Ipomoea pes-caprae Species Convolvulaceae Eukaryota n.a. n.a. n.a. PMID[15730248]
NPO23352 Ipomoea pes-caprae Species Convolvulaceae Eukaryota Leaves Khon Kaen, Thailand 2002-APR PMID[15921434]
NPO23352 Ipomoea pes-caprae Species Convolvulaceae Eukaryota n.a. n.a. n.a. PMID[19061389]
NPO23352 Ipomoea pes-caprae Species Convolvulaceae Eukaryota ground entire plants Hainan Province, China 2004-APR PMID[19061389]
NPO23352 Ipomoea pes-caprae Species Convolvulaceae Eukaryota n.a. aerial part n.a. PMID[21338052]
NPO23352 Ipomoea pes-caprae Species Convolvulaceae Eukaryota n.a. n.a. n.a. PMID[31017778]
NPO23352 Ipomoea pes-caprae Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23352 Ipomoea pes-caprae Species Convolvulaceae 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
NPT389 Cell line RPMI-8226 Homo sapiens IC50 = 7700.0 nM PMID[34969245]
NPT28438 Unchecked Unchecked n.a. Activity n.a. n.a. n.a. PMID[34969245]
NPT28438 Unchecked Unchecked n.a. IC50 > 10000.0 nM PMID[34969245]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. ED50 = 5.0 ug ml-1 PMID[15730248]
NPT25439 Cell line MM1.S Homo sapiens IC50 > 10000.0 nM PMID[34969245]
NPT25439 Cell line MM1.S Homo sapiens Activity n.a. n.a. n.a. PMID[34969245]

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 NPC307400 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
1.0 High Similarity NPC27289
0.9737 High Similarity NPC143421
0.9605 High Similarity NPC477319
0.9494 High Similarity NPC123204
0.9487 High Similarity NPC290012
0.9221 High Similarity NPC267592
0.9125 High Similarity NPC183888
0.9125 High Similarity NPC259294
0.9067 High Similarity NPC113745
0.9067 High Similarity NPC477320
0.9067 High Similarity NPC477323
0.9067 High Similarity NPC477325
0.9067 High Similarity NPC609436
0.8889 High Similarity NPC126685
0.8533 High Similarity NPC146380
0.8519 High Similarity NPC472204
0.8415 Intermediate Similarity NPC483170
0.825 Intermediate Similarity NPC477326
0.8072 Intermediate Similarity NPC119583
0.8 Intermediate Similarity NPC604005
0.8 Intermediate Similarity NPC605014
0.7882 Intermediate Similarity NPC115013
0.7625 Intermediate Similarity NPC281563
0.759 Intermediate Similarity NPC477344
0.7579 Intermediate Similarity NPC10121
0.7579 Intermediate Similarity NPC198918
0.7527 Intermediate Similarity NPC35338
0.7527 Intermediate Similarity NPC204214
0.7527 Intermediate Similarity NPC92283
0.7471 Intermediate Similarity NPC169345
0.747 Intermediate Similarity NPC478734
0.747 Intermediate Similarity NPC89843
0.7386 Intermediate Similarity NPC184915
0.7386 Intermediate Similarity NPC224953
0.734 Intermediate Similarity NPC63404
0.7326 Intermediate Similarity NPC472205
0.7294 Intermediate Similarity NPC478733
0.7273 Intermediate Similarity NPC477317
0.7273 Intermediate Similarity NPC477318
0.7229 Intermediate Similarity NPC22742
0.7229 Intermediate Similarity NPC477346
0.7222 Intermediate Similarity NPC44782
0.7215 Intermediate Similarity NPC606819
0.7176 Intermediate Similarity NPC600446
0.7176 Intermediate Similarity NPC605013
0.7126 Intermediate Similarity NPC297768
0.7053 Intermediate Similarity NPC124878
0.7053 Intermediate Similarity NPC231888
0.7011 Intermediate Similarity NPC146992
0.7011 Intermediate Similarity NPC85759
0.6966 Remote Similarity NPC476087
0.6966 Remote Similarity NPC475667
0.6897 Remote Similarity NPC109887
0.6889 Remote Similarity NPC478732
0.6854 Remote Similarity NPC294748
0.6813 Remote Similarity NPC475270
0.6813 Remote Similarity NPC475327
0.6778 Remote Similarity NPC238264
0.6778 Remote Similarity NPC477345
0.6742 Remote Similarity NPC173328
0.6703 Remote Similarity NPC238056
0.67 Remote Similarity NPC10883
0.6627 Remote Similarity NPC477350
0.6591 Remote Similarity NPC158302
0.6559 Remote Similarity NPC472200
0.6484 Remote Similarity NPC186992
0.6421 Remote Similarity NPC475164
0.6396 Remote Similarity NPC147032
0.6392 Remote Similarity NPC475241
0.6344 Remote Similarity NPC478731
0.6304 Remote Similarity NPC478730
0.6292 Remote Similarity NPC477331
0.6186 Remote Similarity NPC473605
0.6186 Remote Similarity NPC475375
0.6168 Remote Similarity NPC472352
0.6146 Remote Similarity NPC269318
0.6067 Remote Similarity NPC477349
0.6058 Remote Similarity NPC290276
0.5909 Remote Similarity NPC471024
0.5876 Remote Similarity NPC163409
0.5876 Remote Similarity NPC475525
0.5876 Remote Similarity NPC475540
0.587 Remote Similarity NPC479059
0.5816 Remote Similarity NPC476066
0.5769 Remote Similarity NPC77651
0.5755 Remote Similarity NPC611287
0.5741 Remote Similarity NPC600721
0.5741 Remote Similarity NPC605872
0.5701 Remote Similarity NPC600672
0.5684 Remote Similarity NPC479058
0.5667 Remote Similarity NPC477329
0.5636 Remote Similarity NPC600940
0.5632 Remote Similarity NPC478729
0.5619 Remote Similarity NPC28069
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
0.5521 Remote Similarity NPC479060
0.5505 Remote Similarity NPC471025
0.5413 Remote Similarity NPC610996
0.5385 Remote Similarity NPC477328
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
0.5043 Remote Similarity NPC471026

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC307400 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