Natural Product: NPC478150

Natural Product IDNPC478150
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
Xanifolia-Y0
IUPAC Name (2S,3S,4S,5R,6R)-6-[[(3S,4S,4aS,6aR,6bS,7R,8S,8aR,9R,10R,12aS,14aR,14bS)-7,8-dihydroxy-8a-(hydroxymethyl)-4,6a,6b,11,11,14b-hexamethyl-10-[(Z)-2-methylbut-2-enoyl]oxy-9-(2-methylpropanoyloxy)-2,3,4,4a,5,6,7,8,9,10,12,12a,14,14a-tetradecahydro-1H-picen-3-yl]oxy]-4-[(2S,3R,4R,5S)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy-3-hydroxy-5-[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyoxane-2-carboxylic acid
Synonyms Xanifolia-Y0
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 44560532
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001553] Triterpenoids

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 WQGCJSVCEJXKJA-JDJXESOBSA-N
Standard InCHI InChI=1S/C55H86O23/c1-11-23(4)47(70)77-43-44(78-46(69)22(2)3)55(21-58)27(18-51(43,6)7)26-12-13-31-52(8)16-15-28(24(5)25(52)14-17-53(31,9)54(26,10)41(65)42(55)66)71-50-40(76-49-36(63)34(61)32(59)29(19-56)72-49)38(37(64)39(75-50)45(67)68)74-48-35(62)33(60)30(20-57)73-48/h11-12,22,24-25,27-44,48-50,56-66H,13-21H2,1-10H3,(H,67,68)/b23-11-/t24-,25-,27-,28-,29+,30-,31+,32-,33-,34-,35+,36+,37-,38-,39-,40+,41-,42+,43-,44-,48-,49-,50+,52-,53+,54-,55-/m0/s1
SMILES C/C=C(/C)\C(=O)O[C@H]1[C@@H]([C@]2([C@@H](CC1(C)C)C3=CC[C@@H]4[C@]5(CC[C@@H]([C@H]([C@@H]5CC[C@]4([C@@]3([C@H]([C@H]2O)O)C)C)C)O[C@H]6[C@@H]([C@H]([C@@H]([C@H](O6)C(=O)O)O)O[C@H]7[C@@H]([C@H]([C@@H](O7)CO)O)O)O[C@H]8[C@@H]([C@H]([C@H]([C@H](O8)CO)O)O)O)C)CO)OC(=O)C(C)C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1114.56 Volume:   1080.377
?
Van der Waals volume.
Dense:   1.032 LogP:   1.102
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.153
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.183
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   16.0 Rigid Bonds:   47.0
TPSA:   367.81
?
Topological Polar Surface Area.
H-Bond Acceptor:   23.0
H-Bond Donor:   12.0 Rings:   8.0
Heavy Atoms:   23.0

MedChem Properties

QED Drug-Likeness Score:   0.045 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.011 Fsp3:   0.873
MCE-18:   180.893
?
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:   0.745 Fluc inhibitor:   0.007
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.001
?
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:   0.25 Promiscuous compounds:   0.23

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.398 MDCK Permeability:   -5.171
Pgp-inhibitor:   0.0 Pgp-substrate:   0.021
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):   0.038
20% Bioavailability (F20%):   0.976 30% Bioavailability (F30%):   0.989
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.002 MRP1:   0.996
Plasma Protein Binding (PPB):   77.74% Volume Distribution (VD):   -0.475
Fu: 13.858%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   0.999
OATP1B3 inhibitor:   0.008 BCRP inhibitor:   0.0
BSEP inhibitor:   0.003

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:   0.091 CYP3A4-substrate:   0.131
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.187
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):  0.027 Half-life (T1/2):  2.516

ADMET: Toxicity

hERG Blockers:  0.0 hERG Blockers (10um):  0.001
Human Hepatotoxicity (H-HT):  0.617 Drug-induced Liver Injury (DILI):  0.981
AMES Toxicity:  0.973 Rat Oral Acute Toxicity:  0.014
Maximum Recommended Daily Dose:  0.001 Skin Sensitization:  1.0
Carcinogencity:  0.197 Eye Corrosion:  0.0
Eye Irritation:  0.001 Respiratory Toxicity:  0.007
Drug-induced Neurotoxicity:  0.001 Ototoxicity:  0.999
Hematotoxicity:  0.974 Drug-induced Nephrotoxicity:  0.999
Genotoxicity:  0.919 RPMI-8226 Immunitoxicity:  0.241
A549 Cytotoxicity:  0.99 Hek293 Cytotoxicity:  0.6
BCF:   0.356
?
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:   3.378
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.357
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.104
?
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
NPO30992 Xanthoceras sorbifolia Species Sapindaceae Eukaryota wood n.a. n.a. PMID[10691716]
NPO30992 Xanthoceras sorbifolia Species Sapindaceae Eukaryota husks Inner Mongolia, China 2004-SEP PMID[18549275]
NPO30992 Xanthoceras sorbifolia Species Sapindaceae Eukaryota n.a. n.a. n.a. PMID[22801644]
NPO30992 Xanthoceras sorbifolia Species Sapindaceae Eukaryota leaves n.a. n.a. PMID[23313635]
NPO30992 Xanthoceras sorbifolia Species Sapindaceae 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
NPT377 Cell line OVCAR-3 Homo sapiens IC50 = 4200 nM PMID[18549275]

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 NPC478150 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
0.9604 High Similarity NPC478152
0.8182 Intermediate Similarity NPC478155
0.7982 Intermediate Similarity NPC329976
0.7838 Intermediate Similarity NPC478151
0.7417 Intermediate Similarity NPC478153
0.7 Intermediate Similarity NPC46823
0.6942 Remote Similarity NPC192765
0.6885 Remote Similarity NPC178264
0.678 Remote Similarity NPC25998
0.6695 Remote Similarity NPC605294
0.6667 Remote Similarity NPC478154
0.64 Remote Similarity NPC329828
0.6328 Remote Similarity NPC484833
0.632 Remote Similarity NPC473918
0.624 Remote Similarity NPC602995
0.6124 Remote Similarity NPC262796
0.6124 Remote Similarity NPC45346
0.6063 Remote Similarity NPC277212
0.6063 Remote Similarity NPC30279
0.6047 Remote Similarity NPC476780
0.6016 Remote Similarity NPC71391
0.5984 Remote Similarity NPC477077
0.5948 Remote Similarity NPC603026
0.592 Remote Similarity NPC609119
0.5878 Remote Similarity NPC271610
0.5873 Remote Similarity NPC478600
0.5873 Remote Similarity NPC478599
0.5846 Remote Similarity NPC478598
0.582 Remote Similarity NPC470914
0.5789 Remote Similarity NPC475377
0.5789 Remote Similarity NPC476074
0.5789 Remote Similarity NPC476777
0.5656 Remote Similarity NPC470913
0.5649 Remote Similarity NPC329923
0.5649 Remote Similarity NPC475281
0.5635 Remote Similarity NPC477197
0.5547 Remote Similarity NPC329960
0.5441 Remote Similarity NPC329657
0.5354 Remote Similarity NPC477078
0.5349 Remote Similarity NPC107536
0.5349 Remote Similarity NPC280029
0.5349 Remote Similarity NPC9470
0.5338 Remote Similarity NPC47995
0.5333 Remote Similarity NPC488308
0.5333 Remote Similarity NPC476774
0.5324 Remote Similarity NPC488309
0.5294 Remote Similarity NPC225791
0.5294 Remote Similarity NPC312650
0.5255 Remote Similarity NPC484059
0.5255 Remote Similarity NPC484060
0.5245 Remote Similarity NPC150893
0.5221 Remote Similarity NPC265841
0.5217 Remote Similarity NPC110700
0.5185 Remote Similarity NPC475167
0.5185 Remote Similarity NPC82380
0.5185 Remote Similarity NPC244296
0.5161 Remote Similarity NPC605226
0.5156 Remote Similarity NPC477076
0.5147 Remote Similarity NPC134914
0.5147 Remote Similarity NPC473755
0.5147 Remote Similarity NPC484061
0.5147 Remote Similarity NPC484062
0.5145 Remote Similarity NPC476779
0.5143 Remote Similarity NPC476775
0.5072 Remote Similarity NPC475513
0.5072 Remote Similarity NPC329993
0.5037 Remote Similarity NPC264566
0.5036 Remote Similarity NPC470518

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC478150 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