Natural Product: NPC54636

Natural Product IDNPC54636
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
Oleanolic Acid 3-O-{O-Beta-D-Glucopyranosyl-(1->4)-O-Beta-D-Glucopyranosyl-(1->3)-O-Alpha-L-Rhamnopyranosyl-(1->2)-O-Beta-D-Glucopyranosyl-(1->4)-Alpha-L-Arabinopyranoside}
IUPAC Name (4aS,6aR,6aS,6bR,8aR,10S,12aR,14bS)-10-[(2S,3R,4S,5S)-3-[(2S,3R,4R,5S,6S)-4-[(2S,3R,4R,5S,6R)-3,4-dihydroxy-6-(hydroxymethyl)-5-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyoxan-2-yl]oxy-3,5-dihydroxy-6-methyloxan-2-yl]oxy-4-hydroxy-5-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyoxan-2-yl]oxy-2,2,6a,6b,9,9,12a-heptamethyl-1,3,4,5,6,6a,7,8,8a,10,11,12,13,14b-tetradecahydropicene-4a-carboxylic acid
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL524336
PubChem CID 10820194
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 OIIUKDNESXXGGA-JNYGYAQVSA-N
Standard InCHI InChI=1S/C59H96O26/c1-24-34(63)46(84-50-43(72)40(69)45(29(22-62)80-50)83-49-42(71)39(68)36(65)28(21-61)79-49)44(73)51(77-24)85-47-37(66)30(81-48-41(70)38(67)35(64)27(20-60)78-48)23-76-52(47)82-33-12-13-56(6)31(55(33,4)5)11-14-58(8)32(56)10-9-25-26-19-54(2,3)15-17-59(26,53(74)75)18-16-57(25,58)7/h9,24,26-52,60-73H,10-23H2,1-8H3,(H,74,75)/t24-,26-,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-,56-,57+,58+,59-/m0/s1
SMILES OC[C@H]1O[C@@H](O[C@H]2CO[C@H]([C@@H]([C@H]2O)O[C@@H]2O[C@@H](C)[C@@H]([C@H]([C@H]2O)O[C@@H]2O[C@H](CO)[C@H]([C@@H]([C@H]2O)O)O[C@@H]2O[C@H](CO)[C@H]([C@@H]([C@H]2O)O)O)O)O[C@H]2CC[C@]3([C@H](C2(C)C)CC[C@@]2([C@@H]3CC=C3[C@@]2(C)CC[C@@]2([C@H]3CC(C)(C)CC2)C(=O)O)C)C)[C@@H]([C@H]([C@@H]1O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1220.62 Volume:   1166.728
?
Van der Waals volume.
Dense:   1.046 LogP:   0.113
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.32
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.951
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   14.0 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:   0.066 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.189 Fsp3:   0.949
MCE-18:   217.043
?
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:   0.854 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.004
?
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:   0.366 Promiscuous compounds:   0.143

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.944 MDCK Permeability:   -5.118
Pgp-inhibitor:   0.0 Pgp-substrate:   0.032
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):   0.975
20% Bioavailability (F20%):   0.181 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.006 MRP1:   0.006
Plasma Protein Binding (PPB):   66.389% Volume Distribution (VD):   -0.311
Fu: 23.413%
?
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:   0.931 CYP3A4-substrate:   0.008
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.163
HLM stability:   0.0
?
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):  -0.971 Half-life (T1/2):  5.028

ADMET: Toxicity

hERG Blockers:  0.001 hERG Blockers (10um):  0.001
Human Hepatotoxicity (H-HT):  0.865 Drug-induced Liver Injury (DILI):  0.997
AMES Toxicity:  0.986 Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.0 Skin Sensitization:  1.0
Carcinogencity:  0.043 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.777 Drug-induced Nephrotoxicity:  0.992
Genotoxicity:  0.165 RPMI-8226 Immunitoxicity:  0.188
A549 Cytotoxicity:  0.935 Hek293 Cytotoxicity:  0.512
BCF:   1.07
?
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:   3.543
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.102
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.046
?
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
NPO1373 Pulsatilla chinensis Species Ranunculaceae Eukaryota roots n.a. n.a. PMID[10514313]
NPO1373 Pulsatilla chinensis Species Ranunculaceae Eukaryota n.a. root n.a. PMID[10514313]
NPO1373 Pulsatilla chinensis Species Ranunculaceae Eukaryota roots n.a. n.a. PMID[11575962]
NPO1373 Pulsatilla chinensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1373 Pulsatilla chinensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1373 Pulsatilla chinensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1373 Pulsatilla chinensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1373 Pulsatilla chinensis Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO1373 Pulsatilla chinensis Species Ranunculaceae 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
NPT116 Cell line HL-60 Homo sapiens IC50 = 2.7 ug.mL-1 PMID[16933872]
NPT1083 Cell line A-375 Homo sapiens IC50 = 3500.0 nM PMID[17846127]
NPT81 Cell line A549 Homo sapiens IC50 = 6200.0 nM PMID[23249297]
NPT116 Cell line HL-60 Homo sapiens IC50 = 3100.0 nM PMID[22316191]

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 NPC54636 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
0.8889 High Similarity NPC251263
0.8839 High Similarity NPC471385
0.8716 High Similarity NPC166422
0.8411 Intermediate Similarity NPC488564
0.8381 Intermediate Similarity NPC257468
0.8348 Intermediate Similarity NPC161717
0.8288 Intermediate Similarity NPC133818
0.8214 Intermediate Similarity NPC219180
0.8148 Intermediate Similarity NPC324875
0.8148 Intermediate Similarity NPC292677
0.8125 Intermediate Similarity NPC323341
0.7778 Intermediate Similarity NPC139044
0.7568 Intermediate Similarity NPC276093
0.75 Intermediate Similarity NPC471384
0.75 Intermediate Similarity NPC323359
0.7431 Intermediate Similarity NPC114304
0.7232 Intermediate Similarity NPC481082
0.7232 Intermediate Similarity NPC164419
0.7222 Intermediate Similarity NPC127056
0.7143 Intermediate Similarity NPC471383
0.7069 Intermediate Similarity NPC475486
0.7016 Intermediate Similarity NPC43550
0.7009 Intermediate Similarity NPC164194
0.6972 Remote Similarity NPC25605
0.6903 Remote Similarity NPC180550
0.6903 Remote Similarity NPC35405
0.6818 Remote Similarity NPC56713
0.6807 Remote Similarity NPC476992
0.6757 Remote Similarity NPC109079
0.6744 Remote Similarity NPC250247
0.6731 Remote Similarity NPC606107
0.6697 Remote Similarity NPC270667
0.6696 Remote Similarity NPC472949
0.6667 Remote Similarity NPC59804
0.6614 Remote Similarity NPC65105
0.6612 Remote Similarity NPC475287
0.6581 Remote Similarity NPC79718
0.6577 Remote Similarity NPC136877
0.6562 Remote Similarity NPC136768
0.6549 Remote Similarity NPC488561
0.6535 Remote Similarity NPC41061
0.6535 Remote Similarity NPC227551
0.6491 Remote Similarity NPC22956
0.6466 Remote Similarity NPC104400
0.6466 Remote Similarity NPC10320
0.6441 Remote Similarity NPC119794
0.6434 Remote Similarity NPC305981
0.6429 Remote Similarity NPC12288
0.6385 Remote Similarity NPC261506
0.6385 Remote Similarity NPC4328
0.6372 Remote Similarity NPC174679
0.6372 Remote Similarity NPC279554
0.6311 Remote Similarity NPC62725
0.6207 Remote Similarity NPC80843
0.6174 Remote Similarity NPC114441
0.6168 Remote Similarity NPC204407
0.6165 Remote Similarity NPC220160
0.6148 Remote Similarity NPC488209
0.6061 Remote Similarity NPC236638
0.6061 Remote Similarity NPC294453
0.6047 Remote Similarity NPC481080
0.6032 Remote Similarity NPC151543
0.6015 Remote Similarity NPC298034
0.6015 Remote Similarity NPC71065
0.5954 Remote Similarity NPC110633
0.5909 Remote Similarity NPC258617
0.5906 Remote Similarity NPC79643
0.5882 Remote Similarity NPC469945
0.5873 Remote Similarity NPC288205
0.5873 Remote Similarity NPC51465
0.5818 Remote Similarity NPC283849
0.5814 Remote Similarity NPC135904
0.5794 Remote Similarity NPC280941
0.5794 Remote Similarity NPC235772
0.5764 Remote Similarity NPC40085
0.5758 Remote Similarity NPC476068
0.5746 Remote Similarity NPC293330
0.5738 Remote Similarity NPC258885
0.5714 Remote Similarity NPC31839
0.5714 Remote Similarity NPC6377
0.5714 Remote Similarity NPC208381
0.5704 Remote Similarity NPC202828
0.5704 Remote Similarity NPC119592
0.5704 Remote Similarity NPC111466
0.5702 Remote Similarity NPC204392
0.5693 Remote Similarity NPC488212
0.5692 Remote Similarity NPC123199
0.5691 Remote Similarity NPC73829
0.5652 Remote Similarity NPC191410
0.5649 Remote Similarity NPC475160
0.5649 Remote Similarity NPC475140
0.5649 Remote Similarity NPC473714
0.5645 Remote Similarity NPC488515
0.5591 Remote Similarity NPC481078
0.5581 Remote Similarity NPC60557
0.5581 Remote Similarity NPC67857
0.5578 Remote Similarity NPC264270
0.5565 Remote Similarity NPC275668
0.5565 Remote Similarity NPC284807
0.5565 Remote Similarity NPC475504
0.5565 Remote Similarity NPC123796
0.5556 Remote Similarity NPC475514
0.5474 Remote Similarity NPC481081
0.5462 Remote Similarity NPC473824
0.5455 Remote Similarity NPC488516
0.5439 Remote Similarity NPC286347
0.5426 Remote Similarity NPC480939
0.5403 Remote Similarity NPC473383
0.5398 Remote Similarity NPC28198
0.5398 Remote Similarity NPC476123
0.5397 Remote Similarity NPC471435
0.5397 Remote Similarity NPC471434
0.536 Remote Similarity NPC148417
0.5339 Remote Similarity NPC475472
0.5312 Remote Similarity NPC291903
0.5308 Remote Similarity NPC75287
0.5299 Remote Similarity NPC470218
0.5299 Remote Similarity NPC191827
0.5294 Remote Similarity NPC211798
0.5267 Remote Similarity NPC475119
0.5263 Remote Similarity NPC470911
0.5259 Remote Similarity NPC47995
0.5259 Remote Similarity NPC488560
0.5242 Remote Similarity NPC240734
0.5234 Remote Similarity NPC78034
0.5227 Remote Similarity NPC76972
0.5227 Remote Similarity NPC469782
0.5227 Remote Similarity NPC204414
0.5227 Remote Similarity NPC610204
0.52 Remote Similarity NPC309714
0.5182 Remote Similarity NPC57484
0.5161 Remote Similarity NPC76497
0.5159 Remote Similarity NPC173859
0.5159 Remote Similarity NPC148603
0.5156 Remote Similarity NPC484832
0.5154 Remote Similarity NPC295823
0.5154 Remote Similarity NPC174720
0.5154 Remote Similarity NPC475467
0.5149 Remote Similarity NPC165204
0.5128 Remote Similarity NPC100383
0.5125 Remote Similarity NPC481323
0.5125 Remote Similarity NPC469778
0.512 Remote Similarity NPC112352
0.5118 Remote Similarity NPC63159
0.5118 Remote Similarity NPC91838
0.5116 Remote Similarity NPC37134
0.5115 Remote Similarity NPC609281
0.5109 Remote Similarity NPC181066
0.5109 Remote Similarity NPC488211
0.5106 Remote Similarity NPC302543
0.5091 Remote Similarity NPC295941
0.5081 Remote Similarity NPC470512
0.5079 Remote Similarity NPC124296
0.5077 Remote Similarity NPC606145
0.5074 Remote Similarity NPC100639
0.5063 Remote Similarity NPC469776
0.5062 Remote Similarity NPC32723
0.5047 Remote Similarity NPC120840
0.5042 Remote Similarity NPC473538
0.5039 Remote Similarity NPC251768
0.5035 Remote Similarity NPC135849
0.5031 Remote Similarity NPC481324

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC54636 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