Natural Product: NPC36831

Natural Product IDNPC36831
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
Latifoloside G
IUPAC Name [(2S,3R,4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-3-[(2S,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxyoxan-2-yl] (1R,2R,4aS,6aR,6aS,6bR,8aR,10S,12aR,14bS)-1-hydroxy-10-[(2S,3R,4S,5S)-5-hydroxy-4-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-3-[(2S,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxyoxan-2-yl]oxy-1,2,6a,6b,9,9,12a-heptamethyl-2,3,4,5,6,6a,7,8,8a,10,11,12,13,14b-tetradecahydropicene-4a-carboxylate
Synonyms Latifoloside G
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL499381
PubChem CID 44566333
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0002049] Terpene glycosides
          • [CHEMONTID:0001580] Triterpene glycosides
            • [CHEMONTID:0002358] Triterpene saponins

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 XOBMETAHXPDITA-SAAJXQLZSA-N
Standard InCHI InChI=1S/C59H96O26/c1-23-12-17-59(53(74)85-52-45(40(70)36(66)29(21-61)80-52)83-48-41(71)37(67)33(63)24(2)77-48)19-18-56(7)26(47(59)58(23,9)75)10-11-31-55(6)15-14-32(54(4,5)30(55)13-16-57(31,56)8)81-51-46(84-49-42(72)38(68)34(64)25(3)78-49)44(27(62)22-76-51)82-50-43(73)39(69)35(65)28(20-60)79-50/h10,23-25,27-52,60-73,75H,11-22H2,1-9H3/t23-,24+,25+,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+,52+,55+,56-,57-,58-,59+/m1/s1
SMILES C[C@@H]1CC[C@@]2(CC[C@]3(C)C(=CC[C@@H]4[C@@]5(C)CC[C@@H](C(C)(C)[C@@H]5CC[C@@]34C)O[C@H]3[C@@H]([C@H]([C@H](CO3)O)O[C@H]3[C@@H]([C@H]([C@@H]([C@@H](CO)O3)O)O)O)O[C@H]3[C@@H]([C@@H]([C@H]([C@H](C)O3)O)O)O)[C@@H]2[C@]1(C)O)C(=O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O[C@H]1[C@@H]([C@@H]([C@H]([C@H](C)O1)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1220.62 Volume:   1166.728
?
Van der Waals volume.
Dense:   1.046 LogP:   0.8
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.778
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.726
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   13.0 Rigid Bonds:   57.0
TPSA:   412.82
?
Topological Polar Surface Area.
H-Bond Acceptor:   26.0
H-Bond Donor:   15.0 Rings:   10.0
Heavy Atoms:   26.0

MedChem Properties

QED Drug-Likeness Score:   0.054 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.289 Fsp3:   0.949
MCE-18:   219.826
?
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:   0.709 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.013
?
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:   0.347 Promiscuous compounds:   0.176

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.948 MDCK Permeability:   -4.823
Pgp-inhibitor:   0.0 Pgp-substrate:   0.712
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):   0.991
20% Bioavailability (F20%):   0.845 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.005
Plasma Protein Binding (PPB):   63.95% Volume Distribution (VD):   -0.309
Fu: 21.191%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 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:   0.012 CYP3A4-substrate:   0.224
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.017
HLM stability:   0.001
?
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):  -0.896 Half-life (T1/2):  4.294

ADMET: Toxicity

hERG Blockers:  0.001 hERG Blockers (10um):  0.001
Human Hepatotoxicity (H-HT):  0.606 Drug-induced Liver Injury (DILI):  0.933
AMES Toxicity:  0.978 Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.0 Skin Sensitization:  1.0
Carcinogencity:  0.009 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.637 Drug-induced Nephrotoxicity:  0.999
Genotoxicity:  0.2 RPMI-8226 Immunitoxicity:  0.422
A549 Cytotoxicity:  0.861 Hek293 Cytotoxicity:  0.242
BCF:   1.038
?
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:   3.502
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.99
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.017
?
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
NPO33035 ilex kudincha Species Aquifoliaceae Eukaryota n.a. n.a. n.a. PMID[10425145]
NPO33035 ilex kudincha Species Aquifoliaceae Eukaryota n.a. n.a. n.a. PMID[10479318]

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
NPT1214 Individual protein Acyl coenzyme A:cholesterol acyltransferase 1 Homo sapiens Inhibition = 10.6 % PMID[15646539]

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 NPC36831 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
0.8969 High Similarity NPC68175
0.8381 Intermediate Similarity NPC268184
0.802 Intermediate Similarity NPC160415
0.7476 Intermediate Similarity NPC161674
0.7429 Intermediate Similarity NPC46665
0.6792 Remote Similarity NPC58448
0.6635 Remote Similarity NPC204458
0.6606 Remote Similarity NPC112352
0.6216 Remote Similarity NPC263756
0.6207 Remote Similarity NPC481079
0.6195 Remote Similarity NPC480475
0.6148 Remote Similarity NPC100639
0.6075 Remote Similarity NPC47063
0.6071 Remote Similarity NPC469946
0.6066 Remote Similarity NPC135904
0.6063 Remote Similarity NPC481081
0.6019 Remote Similarity NPC189884
0.6019 Remote Similarity NPC138334
0.6018 Remote Similarity NPC75417
0.6 Remote Similarity NPC57484
0.5922 Remote Similarity NPC46388
0.5862 Remote Similarity NPC63159
0.5849 Remote Similarity NPC271138
0.582 Remote Similarity NPC60557
0.582 Remote Similarity NPC67857
0.581 Remote Similarity NPC37739
0.5776 Remote Similarity NPC10607
0.5776 Remote Similarity NPC164389
0.5776 Remote Similarity NPC148603
0.5755 Remote Similarity NPC310014
0.5755 Remote Similarity NPC269315
0.5726 Remote Similarity NPC148417
0.5726 Remote Similarity NPC475591
0.5726 Remote Similarity NPC236870
0.5725 Remote Similarity NPC70809
0.5702 Remote Similarity NPC481078
0.5692 Remote Similarity NPC305981
0.5691 Remote Similarity NPC475287
0.569 Remote Similarity NPC117714
0.5678 Remote Similarity NPC222580
0.5649 Remote Similarity NPC261506
0.5649 Remote Similarity NPC4328
0.5645 Remote Similarity NPC123522
0.5645 Remote Similarity NPC79643
0.5635 Remote Similarity NPC471550
0.562 Remote Similarity NPC80986
0.56 Remote Similarity NPC165204
0.5574 Remote Similarity NPC187290
0.5546 Remote Similarity NPC297263
0.5538 Remote Similarity NPC41061
0.5538 Remote Similarity NPC470876
0.5538 Remote Similarity NPC227551
0.5538 Remote Similarity NPC258617
0.5526 Remote Similarity NPC475516
0.5517 Remote Similarity NPC213674
0.5512 Remote Similarity NPC475160
0.5512 Remote Similarity NPC473714
0.5508 Remote Similarity NPC251768
0.5508 Remote Similarity NPC173859
0.5504 Remote Similarity NPC484061
0.5504 Remote Similarity NPC484062
0.5496 Remote Similarity NPC43550
0.5492 Remote Similarity NPC480473
0.5492 Remote Similarity NPC480474
0.5487 Remote Similarity NPC48499
0.547 Remote Similarity NPC192791
0.5462 Remote Similarity NPC110633
0.5455 Remote Similarity NPC128925
0.5455 Remote Similarity NPC477463
0.5448 Remote Similarity NPC224381
0.5433 Remote Similarity NPC155410
0.5433 Remote Similarity NPC123199
0.5424 Remote Similarity NPC480947
0.5403 Remote Similarity NPC470915
0.5391 Remote Similarity NPC235405
0.5391 Remote Similarity NPC25605
0.5385 Remote Similarity NPC476068
0.5345 Remote Similarity NPC249848
0.5345 Remote Similarity NPC107966
0.5338 Remote Similarity NPC136768
0.5338 Remote Similarity NPC236638
0.5338 Remote Similarity NPC294453
0.5323 Remote Similarity NPC31838
0.5317 Remote Similarity NPC76972
0.5317 Remote Similarity NPC469782
0.5317 Remote Similarity NPC204414
0.531 Remote Similarity NPC214484
0.5294 Remote Similarity NPC30735
0.5294 Remote Similarity NPC250247
0.529 Remote Similarity NPC480422
0.5289 Remote Similarity NPC475504
0.5289 Remote Similarity NPC123796
0.5285 Remote Similarity NPC301449
0.5285 Remote Similarity NPC601290
0.5263 Remote Similarity NPC293330
0.5263 Remote Similarity NPC484059
0.5263 Remote Similarity NPC484060
0.5263 Remote Similarity NPC78046
0.5242 Remote Similarity NPC295823
0.5242 Remote Similarity NPC174720
0.5242 Remote Similarity NPC475467
0.5234 Remote Similarity NPC607265
0.5227 Remote Similarity NPC286457
0.5207 Remote Similarity NPC235438
0.5203 Remote Similarity NPC114484
0.52 Remote Similarity NPC104137
0.52 Remote Similarity NPC26626
0.5185 Remote Similarity NPC298034
0.5185 Remote Similarity NPC71065
0.5175 Remote Similarity NPC90856
0.517 Remote Similarity NPC220838
0.5169 Remote Similarity NPC470512
0.5169 Remote Similarity NPC39211
0.5145 Remote Similarity NPC480417
0.513 Remote Similarity NPC164194
0.5122 Remote Similarity NPC302887
0.512 Remote Similarity NPC96641
0.512 Remote Similarity NPC160452
0.512 Remote Similarity NPC470477
0.512 Remote Similarity NPC163183
0.5116 Remote Similarity NPC470911
0.5115 Remote Similarity NPC277212
0.5115 Remote Similarity NPC30279
0.5115 Remote Similarity NPC488560
0.5109 Remote Similarity NPC484063
0.5109 Remote Similarity NPC484064
0.5102 Remote Similarity NPC45606
0.5085 Remote Similarity NPC127056
0.5083 Remote Similarity NPC223301
0.5083 Remote Similarity NPC171544
0.5082 Remote Similarity NPC162574
0.5079 Remote Similarity NPC469947
0.5079 Remote Similarity NPC480948
0.5076 Remote Similarity NPC85154
0.5041 Remote Similarity NPC470514
0.5041 Remote Similarity NPC257468
0.5041 Remote Similarity NPC309714
0.5041 Remote Similarity NPC30289
0.504 Remote Similarity NPC23275
0.5039 Remote Similarity NPC151543
0.5038 Remote Similarity NPC283417
0.5038 Remote Similarity NPC470218
0.5038 Remote Similarity NPC200049
0.5037 Remote Similarity NPC65105
0.5035 Remote Similarity NPC33012

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC36831 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