Natural Product: NPC114287

Natural Product IDNPC114287
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
Ciwujianoside D2
IUPAC Name [(2S,3R,4S,5S,6R)-6-[[(2R,3R,4R,5S,6R)-6-(acetyloxymethyl)-3,4-dihydroxy-5-[(2S,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxyoxan-2-yl]oxymethyl]-3,4,5-trihydroxyoxan-2-yl] (4aS,6aS,6aS,6bR,8aR,10S,12aR,14bS)-6a,9,9,12a-tetramethyl-2-methylidene-10-[(2S,3R,4S,5S)-3,4,5-trihydroxyoxan-2-yl]oxy-3,4,5,6,6a,6b,7,8,8a,10,11,12,13,14b-tetradecahydro-1H-picene-4a-carboxylate
Synonyms Ciwujianoside D2
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL506729
PubChem CID 44559147
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0002049] Terpene glycosides
          • [CHEMONTID:0001755] Diterpene glycosides

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 QBCOXVISDDNXBQ-SGERFESZSA-N
Standard InCHI InChI=1S/C53H82O22/c1-22-12-15-53(17-16-51(6)25-10-11-32-50(4,5)33(73-46-40(62)35(57)29(55)19-68-46)13-14-52(32,7)26(25)8-9-27(51)28(53)18-22)49(66)75-48-42(64)38(60)36(58)30(71-48)20-69-45-43(65)39(61)44(31(72-45)21-67-24(3)54)74-47-41(63)37(59)34(56)23(2)70-47/h9,23,25-26,28-48,55-65H,1,8,10-21H2,2-7H3/t23-,25+,26-,28-,29-,30+,31+,32-,33-,34-,35-,36+,37+,38-,39+,40+,41+,42+,43+,44+,45+,46-,47-,48-,51-,52+,53-/m0/s1
SMILES C=C1CC[C@@]2(CC[C@@]3(C)[C@@H]4CC[C@H]5C(C)(C)[C@H](CC[C@]5(C)[C@H]4CC=C3[C@@H]2C1)O[C@H]1[C@@H]([C@H]([C@H](CO1)O)O)O)C(=O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO[C@H]2[C@@H]([C@H]([C@@H]([C@@H](COC(=O)C)O2)O[C@H]2[C@@H]([C@@H]([C@H]([C@H](C)O2)O)O)O)O)O)O1)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1070.53 Volume:   1031.075
?
Van der Waals volume.
Dense:   1.038 LogP:   1.694
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.208
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.874
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The logarithm of aqueous solubility value.
Rotatable Bonds:   13.0 Rigid Bonds:   53.0
TPSA:   339.74
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Topological Polar Surface Area.
H-Bond Acceptor:   22.0
H-Bond Donor:   11.0 Rings:   9.0
Heavy Atoms:   22.0

MedChem Properties

QED Drug-Likeness Score:   0.07 GASA:   1.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   6.842 Fsp3:   0.887
MCE-18:   186.26
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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:   0.893 Fluc inhibitor:   0.0
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.005
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.0
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.192 Promiscuous compounds:   0.185

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.139 MDCK Permeability:   -5.049
Pgp-inhibitor:   0.0 Pgp-substrate:   0.671
PAMPA:   0.999
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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):   0.037
20% Bioavailability (F20%):   0.536 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.011 MRP1:   0.003
Plasma Protein Binding (PPB):   63.851% Volume Distribution (VD):   -0.383
Fu: 26.284%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.002
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:   0.989
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.983
HLM stability:   0.185
?
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):  -0.278 Half-life (T1/2):  3.726

ADMET: Toxicity

hERG Blockers:  0.007 hERG Blockers (10um):  0.029
Human Hepatotoxicity (H-HT):  0.367 Drug-induced Liver Injury (DILI):  0.921
AMES Toxicity:  0.986 Rat Oral Acute Toxicity:  0.001
Maximum Recommended Daily Dose:  0.002 Skin Sensitization:  1.0
Carcinogencity:  0.016 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.539 Drug-induced Nephrotoxicity:  0.961
Genotoxicity:  0.063 RPMI-8226 Immunitoxicity:  0.305
A549 Cytotoxicity:  0.951 Hek293 Cytotoxicity:  0.521
BCF:   1.628
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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:   4.193
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   6.079
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   5.205
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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
NPO31494 Acanthopanax senticosus n.a. n.a. n.a. n.a. leaf n.a. PMID[11816040]
NPO31494 Acanthopanax senticosus n.a. n.a. n.a. n.a. n.a. n.a. PMID[17125224]
NPO11872 Eleutherococcus senticosus Species Araliaceae Eukaryota n.a. leaf n.a. PMID[17125224]
NPO11872 Eleutherococcus senticosus Species Araliaceae Eukaryota leaves n.a. n.a. PMID[27400231]
NPO31494 Acanthopanax senticosus n.a. n.a. n.a. Barks Iksan, Chunbuk, Korea n.a. PMID[3127544]
NPO11872 Eleutherococcus senticosus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO31494 Acanthopanax senticosus n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO31494 Acanthopanax senticosus n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO11872 Eleutherococcus senticosus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO31494 Acanthopanax senticosus n.a. n.a. n.a. n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11872 Eleutherococcus senticosus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO11872 Eleutherococcus senticosus Species Araliaceae 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
NPT2797 Individual protein Pancreatic lipase Homo sapiens Inhibition = 46.7 % PMID[17125224]

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 NPC114287 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
0.8857 High Similarity NPC309907
0.8641 High Similarity NPC473826
0.6148 Remote Similarity NPC165204
0.5968 Remote Similarity NPC475209
0.5917 Remote Similarity NPC295823
0.5917 Remote Similarity NPC174720
0.5917 Remote Similarity NPC475467
0.5625 Remote Similarity NPC488560
0.5403 Remote Similarity NPC241909
0.5246 Remote Similarity NPC148417
0.5234 Remote Similarity NPC60557
0.5234 Remote Similarity NPC67857
0.5227 Remote Similarity NPC481080
0.5191 Remote Similarity NPC475160
0.5191 Remote Similarity NPC473714
0.5147 Remote Similarity NPC236638
0.5147 Remote Similarity NPC294453
0.5115 Remote Similarity NPC135904
0.5108 Remote Similarity NPC250247
0.5037 Remote Similarity NPC110633
0.5036 Remote Similarity NPC136768
0.5036 Remote Similarity NPC224381

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC114287 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