Natural Product: NPC60849

Natural Product IDNPC60849
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
Albinoside I
IUPAC Name n.a.
Synonyms Albinoside I
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL2146618
PubChem CID 71452845
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 IZXAJJIHCIQBDV-QZAYOBNPSA-N
Standard InCHI InChI=1S/C51H86O26/c1-9-17-28-18-15-13-11-10-12-14-16-19-30(54)73-45-39(63)41(74-46(64)21(2)22(3)52)26(7)69-50(45)76-42-34(58)31(55)23(4)66-48(42)65-20-29-33(57)36(60)44(75-47-38(62)37(61)40(25(6)68-47)70-27(8)53)51(72-29)77-43-35(59)32(56)24(5)67-49(43)71-28/h21-26,28-29,31-45,47-52,55-63H,9-20H2,1-8H3/t21-,22-,23-,24-,25+,26+,28+,29-,31-,32-,33-,34+,35+,36+,37+,38-,39-,40+,41+,42-,43-,44-,45-,47+,48-,49+,50+,51+/m1/s1
SMILES CCC[C@H]1CCCCCCCCCC(=O)O[C@H]2[C@H](O[C@H]3[C@H](OC[C@H]4O[C@@H](O[C@H]5[C@H](O1)O[C@H](C)[C@H]([C@@H]5O)O)[C@H](O[C@@H]1O[C@@H](C)[C@@H]([C@H]([C@H]1O)O)OC(=O)C)[C@H]([C@@H]4O)O)O[C@H](C)[C@H]([C@@H]3O)O)O[C@H]([C@@H]([C@H]2O)OC(=O)[C@@H]([C@H](O)C)C)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1114.54 Volume:   1059.949
?
Van der Waals volume.
Dense:   1.052 LogP:   1.348
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.817
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -2.484
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   10.0 Rigid Bonds:   54.0
TPSA:   373.5
?
Topological Polar Surface Area.
H-Bond Acceptor:   26.0
H-Bond Donor:   10.0 Rings:   6.0
Heavy Atoms:   26.0

MedChem Properties

QED Drug-Likeness Score:   0.099 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.982 Fsp3:   0.941
MCE-18:   133.636
?
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:   0.661 Fluc inhibitor:   0.334
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.006
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.0
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.534 Promiscuous compounds:   0.205

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.022 MDCK Permeability:   -4.899
Pgp-inhibitor:   0.0 Pgp-substrate:   0.655
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):   0.001
20% Bioavailability (F20%):   0.0 30% Bioavailability (F30%):   0.308
50% Bioavailability (F50%):   0.577

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.675
Plasma Protein Binding (PPB):   49.044% Volume Distribution (VD):   -0.407
Fu: 38.053%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.0
BSEP inhibitor:   0.027

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:   0.0 CYP3A4-substrate:   0.299
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.137
HLM stability:   0.744
?
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):  0.064 Half-life (T1/2):  4.342

ADMET: Toxicity

hERG Blockers:  0.001 hERG Blockers (10um):  0.011
Human Hepatotoxicity (H-HT):  0.839 Drug-induced Liver Injury (DILI):  1.0
AMES Toxicity:  0.95 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:  1.0
Hematotoxicity:  0.475 Drug-induced Nephrotoxicity:  0.998
Genotoxicity:  0.001 RPMI-8226 Immunitoxicity:  0.742
A549 Cytotoxicity:  0.919 Hek293 Cytotoxicity:  0.049
BCF:   0.424
?
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:   3.155
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.84
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   3.815
?
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
NPO13214 Ipomoea alba Species Convolvulaceae Eukaryota seeds n.a. n.a. PMID[22924480]
NPO13214 Ipomoea alba Species Convolvulaceae Eukaryota Seeds n.a. n.a. PMID[28006904]
NPO13214 Ipomoea alba Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13214 Ipomoea alba 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
NPT83 Cell line MCF7 Homo sapiens IC50 > 20.0 ug.mL-1 PMID[22924480]
NPT2 Others Unspecified n.a. FC = 4.2 n.a. PMID[22924480]
NPT2 Others Unspecified n.a. FC = 3.1 n.a. PMID[22924480]
NPT2 Others Unspecified n.a. FC = 2.1 n.a. PMID[22924480]

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 NPC60849 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
0.8375 Intermediate Similarity NPC479058
0.7209 Intermediate Similarity NPC478730
0.7143 Intermediate Similarity NPC479059
0.7045 Intermediate Similarity NPC478732
0.7045 Intermediate Similarity NPC478731
0.7024 Intermediate Similarity NPC477332
0.6966 Remote Similarity NPC475270
0.6966 Remote Similarity NPC475327
0.6932 Remote Similarity NPC476087
0.6932 Remote Similarity NPC475667
0.663 Remote Similarity NPC476066
0.6522 Remote Similarity NPC475525
0.6522 Remote Similarity NPC475540
0.6489 Remote Similarity NPC473605
0.6489 Remote Similarity NPC475375
0.6429 Remote Similarity NPC477328
0.6383 Remote Similarity NPC475164
0.6333 Remote Similarity NPC297768
0.6264 Remote Similarity NPC119583
0.625 Remote Similarity NPC477331
0.6196 Remote Similarity NPC483170
0.6145 Remote Similarity NPC478729
0.6129 Remote Similarity NPC115013
0.6125 Remote Similarity NPC479056
0.6105 Remote Similarity NPC269318
0.6064 Remote Similarity NPC224953
0.6047 Remote Similarity NPC477330
0.6044 Remote Similarity NPC478722
0.602 Remote Similarity NPC475241
0.5978 Remote Similarity NPC479060
0.5977 Remote Similarity NPC477329
0.5962 Remote Similarity NPC610996
0.5952 Remote Similarity NPC606819
0.5934 Remote Similarity NPC109887
0.5914 Remote Similarity NPC186992
0.5889 Remote Similarity NPC478734
0.587 Remote Similarity NPC479061
0.5824 Remote Similarity NPC477344
0.5806 Remote Similarity NPC173328
0.5773 Remote Similarity NPC477347
0.5761 Remote Similarity NPC478733
0.5741 Remote Similarity NPC610997
0.5729 Remote Similarity NPC479057
0.5729 Remote Similarity NPC184915
0.5714 Remote Similarity NPC89843
0.5714 Remote Similarity NPC478728
0.5714 Remote Similarity NPC611287
0.5699 Remote Similarity NPC267592
0.566 Remote Similarity NPC600672
0.5657 Remote Similarity NPC478727
0.5638 Remote Similarity NPC478723
0.5625 Remote Similarity NPC477317
0.5625 Remote Similarity NPC477318
0.5612 Remote Similarity NPC44782
0.5579 Remote Similarity NPC143421
0.5579 Remote Similarity NPC307400
0.5579 Remote Similarity NPC27289
0.5568 Remote Similarity NPC475425
0.5556 Remote Similarity NPC600721
0.5556 Remote Similarity NPC605872
0.5532 Remote Similarity NPC478725
0.5521 Remote Similarity NPC238264
0.5521 Remote Similarity NPC477345
0.551 Remote Similarity NPC472200
0.5495 Remote Similarity NPC113745
0.5495 Remote Similarity NPC477320
0.5495 Remote Similarity NPC477323
0.5495 Remote Similarity NPC477325
0.5495 Remote Similarity NPC609436
0.5474 Remote Similarity NPC478724
0.5474 Remote Similarity NPC477319
0.5464 Remote Similarity NPC169345
0.5464 Remote Similarity NPC290012
0.5455 Remote Similarity NPC600940
0.5444 Remote Similarity NPC281563
0.5408 Remote Similarity NPC183888
0.5408 Remote Similarity NPC126685
0.5361 Remote Similarity NPC478726
0.5354 Remote Similarity NPC123204
0.5319 Remote Similarity NPC158302
0.5319 Remote Similarity NPC477326
0.5312 Remote Similarity NPC472205
0.5306 Remote Similarity NPC238056
0.52 Remote Similarity NPC163409
0.5161 Remote Similarity NPC87153
0.5158 Remote Similarity NPC600446
0.5158 Remote Similarity NPC605013
0.5155 Remote Similarity NPC44682
0.5146 Remote Similarity NPC477348
0.51 Remote Similarity NPC259294
0.5063 Remote Similarity NPC206823
0.5055 Remote Similarity NPC146380

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC60849 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