Natural Product: NPC110633

Natural Product IDNPC110633
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
3-O-Beta-D-Xylopyranosyl-(1->3)-Alpha-L-Rhamnopyranosyl-(1->2)-Alpha-L-Arabinopyranosylsiaresinolic Acid 28-O-Alpha-L-Rhamnopyranosyl-(1->4)-Beta-Dglucopyranosyl-(1->6)-Beta-D-Glucopyranosyl Ester
IUPAC Name [(2S,3R,4S,5S,6R)-6-[[(2R,3R,4R,5S,6R)-3,4-dihydroxy-6-(hydroxymethyl)-5-[(2S,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxyoxan-2-yl]oxymethyl]-3,4,5-trihydroxyoxan-2-yl] (1S,4aR,6aR,6aS,6bR,8aR,10S,12aR,14bS)-10-[(2S,3R,4S,5S)-3-[(2S,3R,4R,5S,6S)-3,5-dihydroxy-6-methyl-4-[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxyoxan-2-yl]oxy-4,5-dihydroxyoxan-2-yl]oxy-1-hydroxy-2,2,6a,6b,9,9,12a-heptamethyl-1,3,4,5,6,6a,7,8,8a,10,11,12,13,14b-tetradecahydropicene-4a-carboxylate
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL2430033
PubChem CID 72189233
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 ANZUJNAJUBXIKU-WFXPECHOSA-N
Standard InCHI InChI=1S/C64H104O30/c1-24-35(68)40(73)44(77)54(86-24)91-48-29(20-65)88-52(46(79)42(48)75)85-23-30-39(72)41(74)45(78)55(89-30)94-58(82)64-18-16-59(3,4)51(81)34(64)26-10-11-32-61(7)14-13-33(60(5,6)31(61)12-15-63(32,9)62(26,8)17-19-64)90-57-50(38(71)28(67)22-84-57)93-56-47(80)49(36(69)25(2)87-56)92-53-43(76)37(70)27(66)21-83-53/h10,24-25,27-57,65-81H,11-23H2,1-9H3/t24-,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+,53-,54-,55-,56-,57-,61-,62+,63+,64-/m0/s1
SMILES OC[C@H]1O[C@@H](OC[C@H]2O[C@@H](OC(=O)[C@]34CC[C@@]5(C(=CC[C@H]6[C@@]5(C)CC[C@@H]5[C@]6(C)CC[C@@H](C5(C)C)O[C@@H]5OC[C@@H]([C@@H]([C@H]5O[C@@H]5O[C@@H](C)[C@@H]([C@H]([C@H]5O)O[C@@H]5OC[C@H]([C@@H]([C@H]5O)O)O)O)O)O)[C@@H]4[C@@H](C(CC3)(C)C)O)C)[C@@H]([C@H]([C@@H]2O)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)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1352.66 Volume:   1279.812
?
Van der Waals volume.
Dense:   1.057 LogP:   0.833
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.549
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.27
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   15.0 Rigid Bonds:   63.0
TPSA:   471.74
?
Topological Polar Surface Area.
H-Bond Acceptor:   30.0
H-Bond Donor:   17.0 Rings:   11.0
Heavy Atoms:   30.0

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:   7.701 Fsp3:   0.953
MCE-18:   240.8
?
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:   0.708 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.023
?
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:   0.377 Promiscuous compounds:   0.047

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -7.054 MDCK Permeability:   -4.864
Pgp-inhibitor:   0.0 Pgp-substrate:   0.98
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):   0.998
20% Bioavailability (F20%):   0.947 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.002
Plasma Protein Binding (PPB):   49.778% Volume Distribution (VD):   -0.275
Fu: 21.041%
?
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:   0.0 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.149
HLM stability:   0.051
?
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):  -1.19 Half-life (T1/2):  4.804

ADMET: Toxicity

hERG Blockers:  0.001 hERG Blockers (10um):  0.003
Human Hepatotoxicity (H-HT):  0.528 Drug-induced Liver Injury (DILI):  0.968
AMES Toxicity:  0.968 Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.0 Skin Sensitization:  1.0
Carcinogencity:  0.001 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.589 Drug-induced Nephrotoxicity:  0.999
Genotoxicity:  0.094 RPMI-8226 Immunitoxicity:  0.609
A549 Cytotoxicity:  0.83 Hek293 Cytotoxicity:  0.235
BCF:   1.048
?
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:   3.447
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.985
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   3.91
?
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
NPO32682 anemone taipaiensis Species Ranunculaceae Eukaryota rhizomes n.a. n.a. PMID[23992864]
NPO32682 anemone taipaiensis Species Ranunculaceae 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
NPT165 Cell line HeLa Homo sapiens IC50 > 80000.0 nM PMID[18676884]
NPT81 Cell line A549 Homo sapiens IC50 > 80000.0 nM DrugMatrix in vivo data: Pathology
NPT116 Cell line HL-60 Homo sapiens IC50 > 80000.0 nM PMID[18077363]
NPT65 Cell line HepG2 Homo sapiens IC50 > 80000.0 nM DOI[10.6019/CHEMBL1201861]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. IC50 = 34780.0 nM PMID[23992864]

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 NPC110633 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
0.9196 High Similarity NPC136768
0.8696 High Similarity NPC236638
0.8696 High Similarity NPC294453
0.8376 Intermediate Similarity NPC305981
0.8305 Intermediate Similarity NPC261506
0.8305 Intermediate Similarity NPC4328
0.8205 Intermediate Similarity NPC41061
0.8205 Intermediate Similarity NPC227551
0.8099 Intermediate Similarity NPC250247
0.8067 Intermediate Similarity NPC202828
0.8067 Intermediate Similarity NPC119592
0.7739 Intermediate Similarity NPC60557
0.7739 Intermediate Similarity NPC67857
0.7727 Intermediate Similarity NPC148417
0.7705 Intermediate Similarity NPC298034
0.7705 Intermediate Similarity NPC71065
0.7692 Intermediate Similarity NPC135904
0.7692 Intermediate Similarity NPC123199
0.7686 Intermediate Similarity NPC43550
0.7647 Intermediate Similarity NPC481080
0.7607 Intermediate Similarity NPC165204
0.7581 Intermediate Similarity NPC220160
0.7521 Intermediate Similarity NPC79643
0.7273 Intermediate Similarity NPC488560
0.7241 Intermediate Similarity NPC295823
0.7241 Intermediate Similarity NPC174720
0.7241 Intermediate Similarity NPC475467
0.72 Intermediate Similarity NPC481081
0.7179 Intermediate Similarity NPC481078
0.7143 Intermediate Similarity NPC475287
0.7143 Intermediate Similarity NPC76972
0.7143 Intermediate Similarity NPC469782
0.7143 Intermediate Similarity NPC204414
0.712 Intermediate Similarity NPC65105
0.6984 Remote Similarity NPC161717
0.6911 Remote Similarity NPC475160
0.6911 Remote Similarity NPC473714
0.688 Remote Similarity NPC476068
0.6853 Remote Similarity NPC469776
0.6828 Remote Similarity NPC32723
0.6781 Remote Similarity NPC481323
0.6781 Remote Similarity NPC469778
0.6719 Remote Similarity NPC293330
0.6689 Remote Similarity NPC135334
0.6667 Remote Similarity NPC63159
0.6667 Remote Similarity NPC241909
0.6609 Remote Similarity NPC161674
0.6606 Remote Similarity NPC128925
0.6533 Remote Similarity NPC481324
0.6515 Remote Similarity NPC224381
0.6512 Remote Similarity NPC258617
0.6484 Remote Similarity NPC57484
0.6471 Remote Similarity NPC295941
0.641 Remote Similarity NPC112352
0.6395 Remote Similarity NPC469775
0.6376 Remote Similarity NPC469774
0.6356 Remote Similarity NPC160415
0.6316 Remote Similarity NPC70809
0.6299 Remote Similarity NPC251263
0.6299 Remote Similarity NPC155410
0.625 Remote Similarity NPC100639
0.625 Remote Similarity NPC100925
0.6179 Remote Similarity NPC481079
0.6172 Remote Similarity NPC219180
0.6169 Remote Similarity NPC469777
0.6136 Remote Similarity NPC475514
0.6094 Remote Similarity NPC471384
0.6087 Remote Similarity NPC480422
0.6051 Remote Similarity NPC469772
0.6033 Remote Similarity NPC101744
0.6018 Remote Similarity NPC256798
0.6016 Remote Similarity NPC192600
0.5975 Remote Similarity NPC469773
0.597 Remote Similarity NPC471385
0.5954 Remote Similarity NPC54636
0.595 Remote Similarity NPC104071
0.5935 Remote Similarity NPC475504
0.5923 Remote Similarity NPC475209
0.5902 Remote Similarity NPC102439
0.5846 Remote Similarity NPC133818
0.5827 Remote Similarity NPC102505
0.5827 Remote Similarity NPC473826
0.5827 Remote Similarity NPC488514
0.5802 Remote Similarity NPC166422
0.5785 Remote Similarity NPC469946
0.5772 Remote Similarity NPC480475
0.5763 Remote Similarity NPC48499
0.576 Remote Similarity NPC134835
0.5704 Remote Similarity NPC13998
0.5704 Remote Similarity NPC286457
0.568 Remote Similarity NPC481082
0.568 Remote Similarity NPC164419
0.5669 Remote Similarity NPC324875
0.5669 Remote Similarity NPC292677
0.5652 Remote Similarity NPC309223
0.5645 Remote Similarity NPC46665
0.5608 Remote Similarity NPC472268
0.56 Remote Similarity NPC68175
0.5591 Remote Similarity NPC73318
0.5574 Remote Similarity NPC295371
0.5556 Remote Similarity NPC297263
0.5546 Remote Similarity NPC78046
0.5541 Remote Similarity NPC297950
0.554 Remote Similarity NPC302543
0.5522 Remote Similarity NPC470218
0.5522 Remote Similarity NPC471550
0.552 Remote Similarity NPC173859
0.552 Remote Similarity NPC148603
0.5489 Remote Similarity NPC470911
0.5462 Remote Similarity NPC204458
0.5462 Remote Similarity NPC90856
0.5462 Remote Similarity NPC475486
0.5462 Remote Similarity NPC31838
0.5462 Remote Similarity NPC36831
0.5462 Remote Similarity NPC187290
0.5448 Remote Similarity NPC309907
0.5441 Remote Similarity NPC85154
0.5435 Remote Similarity NPC470876
0.543 Remote Similarity NPC45606
0.5426 Remote Similarity NPC301449
0.5426 Remote Similarity NPC601290
0.5417 Remote Similarity NPC8524
0.5414 Remote Similarity NPC123522
0.5391 Remote Similarity NPC601659
0.5379 Remote Similarity NPC33012
0.5373 Remote Similarity NPC323341
0.5355 Remote Similarity NPC478559
0.5355 Remote Similarity NPC478560
0.535 Remote Similarity NPC472269
0.5344 Remote Similarity NPC104137
0.5344 Remote Similarity NPC26626
0.5338 Remote Similarity NPC268184
0.5338 Remote Similarity NPC489208
0.5294 Remote Similarity NPC220838
0.5294 Remote Similarity NPC191827
0.529 Remote Similarity NPC21691
0.5285 Remote Similarity NPC475516
0.5276 Remote Similarity NPC164389
0.5276 Remote Similarity NPC488526
0.5276 Remote Similarity NPC232237
0.5271 Remote Similarity NPC469821
0.5267 Remote Similarity NPC480473
0.5267 Remote Similarity NPC480474
0.5252 Remote Similarity NPC473452
0.5252 Remote Similarity NPC480418
0.5242 Remote Similarity NPC58448
0.5238 Remote Similarity NPC223301
0.5238 Remote Similarity NPC171544
0.5234 Remote Similarity NPC105800
0.5231 Remote Similarity NPC104372
0.5231 Remote Similarity NPC276093
0.5227 Remote Similarity NPC207738
0.5221 Remote Similarity NPC480419
0.5217 Remote Similarity NPC4749
0.52 Remote Similarity NPC470512
0.5197 Remote Similarity NPC309714
0.5188 Remote Similarity NPC470915
0.5182 Remote Similarity NPC283417
0.5182 Remote Similarity NPC200049
0.5172 Remote Similarity NPC480417
0.5159 Remote Similarity NPC263756
0.5159 Remote Similarity NPC213674
0.5156 Remote Similarity NPC104400
0.5156 Remote Similarity NPC10320
0.5156 Remote Similarity NPC473459
0.5154 Remote Similarity NPC484832
0.5149 Remote Similarity NPC185466
0.5137 Remote Similarity NPC489209
0.512 Remote Similarity NPC473373
0.5115 Remote Similarity NPC37134
0.5115 Remote Similarity NPC114484
0.5111 Remote Similarity NPC473824
0.5088 Remote Similarity NPC191763
0.5078 Remote Similarity NPC30735
0.5077 Remote Similarity NPC222580
0.5068 Remote Similarity NPC477464
0.5067 Remote Similarity NPC475368
0.504 Remote Similarity NPC235405
0.504 Remote Similarity NPC56713
0.5039 Remote Similarity NPC10607
0.5039 Remote Similarity NPC251768
0.5038 Remote Similarity NPC80986
0.5038 Remote Similarity NPC488515
0.5037 Remote Similarity NPC114287
0.5037 Remote Similarity NPC475119
0.503 Remote Similarity NPC488203

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC110633 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