Natural Product: NPC23275

Natural Product IDNPC23275
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
Rel-Camellioside E
IUPAC Name (2S,3S,4S,5R,6R)-6-[[(3S,4aR,6aR,6bS,8R,8aR,12aS,14aR,14bR)-8,8a-dihydroxy-4,4,6a,6b,11,11,14b-heptamethyl-1,2,3,4a,5,6,7,8,9,10,12,12a,14,14a-tetradecahydropicen-3-yl]oxy]-4-[(2S,3R,4S,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)-3-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyoxan-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 Rel-Camellioside E
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL2087223
PubChem CID 66553431
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 HBDLKPJBPGZZHU-QRQUFXRISA-N
Standard InCHI InChI=1S/C53H86O24/c1-48(2)14-15-53(69)22(16-48)21-8-9-27-50(5)12-11-29(49(3,4)26(50)10-13-51(27,6)52(21,7)17-28(53)57)73-47-42(77-45-37(65)34(62)31(59)24(19-55)71-45)39(38(66)40(75-47)43(67)68)74-46-41(35(63)32(60)25(20-56)72-46)76-44-36(64)33(61)30(58)23(18-54)70-44/h8,22-42,44-47,54-66,69H,9-20H2,1-7H3,(H,67,68)/t22-,23+,24+,25+,26-,27+,28+,29-,30+,31-,32-,33-,34-,35-,36+,37+,38-,39-,40-,41+,42+,44-,45-,46-,47+,50-,51+,52+,53+/m0/s1
SMILES CC1(C)CC[C@]2([C@@H](C1)C1=CC[C@@H]3[C@@]4(C)CC[C@@H](C(C)(C)[C@@H]4CC[C@@]3(C)[C@]1(C)C[C@H]2O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](C(=O)O)O1)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](CO)O1)O)O)O)O[C@H]1[C@@H]([C@H]([C@H]([C@@H](CO)O1)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1106.55 Volume:   1053.928
?
Van der Waals volume.
Dense:   1.05 LogP:   -0.005
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.383
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.231
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   12.0 Rigid Bonds:   51.0
TPSA:   394.36
?
Topological Polar Surface Area.
H-Bond Acceptor:   24.0
H-Bond Donor:   15.0 Rings:   9.0
Heavy Atoms:   24.0

MedChem Properties

QED Drug-Likeness Score:   0.07 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   6.89 Fsp3:   0.943
MCE-18:   199.922
?
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:   0.682 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.003
?
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:   0.155

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.646 MDCK Permeability:   -5.076
Pgp-inhibitor:   0.0 Pgp-substrate:   0.556
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):   1.0
20% Bioavailability (F20%):   0.999 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.947
Plasma Protein Binding (PPB):   57.827% Volume Distribution (VD):   -0.41
Fu: 28.154%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   0.94 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:   0.045
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):  -0.324 Half-life (T1/2):  3.151

ADMET: Toxicity

hERG Blockers:  0.0 hERG Blockers (10um):  0.0
Human Hepatotoxicity (H-HT):  0.869 Drug-induced Liver Injury (DILI):  0.987
AMES Toxicity:  0.992 Rat Oral Acute Toxicity:  0.002
Maximum Recommended Daily Dose:  0.0 Skin Sensitization:  1.0
Carcinogencity:  0.311 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.002
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.956 Drug-induced Nephrotoxicity:  1.0
Genotoxicity:  0.917 RPMI-8226 Immunitoxicity:  0.263
A549 Cytotoxicity:  0.997 Hek293 Cytotoxicity:  0.696
BCF:   0.689
?
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:   3.24
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.598
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   3.57
?
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
NPO23380 Camellia japonica Species Theaceae Eukaryota n.a. leaf n.a. PMID[16926516]
NPO23380 Camellia japonica Species Theaceae Eukaryota flower buds n.a. n.a. PMID[22834923]
NPO23380 Camellia japonica Species Theaceae Eukaryota Roots n.a. n.a. PMID[30395460]
NPO23380 Camellia japonica Species Theaceae Eukaryota n.a. n.a. n.a. PMID[32569471]
NPO23380 Camellia japonica Species Theaceae Eukaryota n.a. n.a. n.a. PMID[39065796]
NPO23380 Camellia japonica Species Theaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23380 Camellia japonica Species Theaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23380 Camellia japonica Species Theaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23380 Camellia japonica Species Theaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23380 Camellia japonica Species Theaceae 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
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Activity = 1.9 % PMID[22834923]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Activity = 4.3 % PMID[22834923]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Activity = 13.3 % PMID[22834923]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Activity = 108.3 % PMID[22834923]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Activity = 110.0 % PMID[22834923]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Activity = 116.2 % PMID[22834923]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Activity = 113.9 % PMID[22834923]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Activity = 110.6 % PMID[22834923]
NPT20529 Non-molecular NON-PROTEIN TARGET n.a. Activity = 114.9 % PMID[22834923]
NPT2 Others Unspecified n.a. Activity = 21.9 % DOI[10.6019/CHEMBL1201861]
NPT2 Others Unspecified n.a. Activity = 16.7 % DOI[10.6019/CHEMBL1201861]
NPT2 Others Unspecified n.a. Activity = 23.3 % DOI[10.6019/CHEMBL1201861]

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 NPC23275 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
0.8077 Intermediate Similarity NPC469947
0.8077 Intermediate Similarity NPC480948
0.7692 Intermediate Similarity NPC302887
0.7477 Intermediate Similarity NPC160452
0.7434 Intermediate Similarity NPC181066
0.7027 Intermediate Similarity NPC480939
0.6759 Remote Similarity NPC44716
0.6726 Remote Similarity NPC480936
0.6667 Remote Similarity NPC480947
0.6636 Remote Similarity NPC22956
0.6545 Remote Similarity NPC475591
0.6545 Remote Similarity NPC236870
0.6525 Remote Similarity NPC283417
0.6525 Remote Similarity NPC200049
0.6514 Remote Similarity NPC605226
0.6475 Remote Similarity NPC484059
0.6475 Remote Similarity NPC484060
0.6364 Remote Similarity NPC484061
0.6364 Remote Similarity NPC484062
0.627 Remote Similarity NPC484063
0.627 Remote Similarity NPC484064
0.6226 Remote Similarity NPC164194
0.6207 Remote Similarity NPC187290
0.6198 Remote Similarity NPC277212
0.6198 Remote Similarity NPC30279
0.6091 Remote Similarity NPC603026
0.6066 Remote Similarity NPC46823
0.6048 Remote Similarity NPC265841
0.6036 Remote Similarity NPC80843
0.6 Remote Similarity NPC225791
0.6 Remote Similarity NPC64715
0.5966 Remote Similarity NPC25998
0.5946 Remote Similarity NPC472949
0.592 Remote Similarity NPC488308
0.5917 Remote Similarity NPC609119
0.5909 Remote Similarity NPC25605
0.5877 Remote Similarity NPC251768
0.5873 Remote Similarity NPC271610
0.5873 Remote Similarity NPC312650
0.5859 Remote Similarity NPC302543
0.5856 Remote Similarity NPC109079
0.5841 Remote Similarity NPC192791
0.5833 Remote Similarity NPC288205
0.5833 Remote Similarity NPC51465
0.5789 Remote Similarity NPC114304
0.5726 Remote Similarity NPC602995
0.5714 Remote Similarity NPC127056
0.5691 Remote Similarity NPC284449
0.569 Remote Similarity NPC118440
0.568 Remote Similarity NPC47995
0.5664 Remote Similarity NPC488561
0.566 Remote Similarity NPC31839
0.5649 Remote Similarity NPC488309
0.5635 Remote Similarity NPC71391
0.5635 Remote Similarity NPC329828
0.563 Remote Similarity NPC301449
0.563 Remote Similarity NPC601290
0.5593 Remote Similarity NPC79718
0.5591 Remote Similarity NPC21691
0.5574 Remote Similarity NPC475119
0.5546 Remote Similarity NPC114692
0.5537 Remote Similarity NPC329976
0.5537 Remote Similarity NPC475486
0.5517 Remote Similarity NPC30289
0.5512 Remote Similarity NPC4749
0.5512 Remote Similarity NPC192765
0.5508 Remote Similarity NPC131469
0.55 Remote Similarity NPC291903
0.5492 Remote Similarity NPC605294
0.5478 Remote Similarity NPC469946
0.5469 Remote Similarity NPC178264
0.5462 Remote Similarity NPC95437
0.5462 Remote Similarity NPC476779
0.544 Remote Similarity NPC477465
0.5433 Remote Similarity NPC473918
0.5426 Remote Similarity NPC476774
0.5426 Remote Similarity NPC476780
0.5417 Remote Similarity NPC236657
0.5403 Remote Similarity NPC313110
0.5398 Remote Similarity NPC12288
0.5345 Remote Similarity NPC213674
0.5339 Remote Similarity NPC159309
0.5339 Remote Similarity NPC480475
0.5339 Remote Similarity NPC86222
0.5327 Remote Similarity NPC606107
0.5315 Remote Similarity NPC480943
0.5303 Remote Similarity NPC110700
0.5303 Remote Similarity NPC476777
0.528 Remote Similarity NPC473824
0.5267 Remote Similarity NPC258617
0.5259 Remote Similarity NPC157868
0.5254 Remote Similarity NPC117714
0.5246 Remote Similarity NPC324875
0.5246 Remote Similarity NPC292677
0.5242 Remote Similarity NPC11242
0.5238 Remote Similarity NPC151543
0.5224 Remote Similarity NPC476775
0.5217 Remote Similarity NPC59804
0.5207 Remote Similarity NPC488515
0.5203 Remote Similarity NPC187618
0.5203 Remote Similarity NPC120116
0.5169 Remote Similarity NPC112352
0.5164 Remote Similarity NPC114484
0.5156 Remote Similarity NPC251263
0.5147 Remote Similarity NPC279915
0.5147 Remote Similarity NPC476778
0.5124 Remote Similarity NPC222580
0.5124 Remote Similarity NPC257468
0.5124 Remote Similarity NPC123796
0.512 Remote Similarity NPC62725
0.5118 Remote Similarity NPC123522
0.5116 Remote Similarity NPC470218
0.5115 Remote Similarity NPC470518
0.5109 Remote Similarity NPC476776
0.5086 Remote Similarity NPC56713
0.5085 Remote Similarity NPC263756
0.5083 Remote Similarity NPC40775
0.5083 Remote Similarity NPC164389
0.5083 Remote Similarity NPC2370
0.5081 Remote Similarity NPC488564
0.5081 Remote Similarity NPC480473
0.5081 Remote Similarity NPC480474
0.5079 Remote Similarity NPC470475
0.5042 Remote Similarity NPC75417
0.5041 Remote Similarity NPC281148
0.5041 Remote Similarity NPC63159
0.504 Remote Similarity NPC36831
0.5039 Remote Similarity NPC268184
0.5038 Remote Similarity NPC470876

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC23275 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