Natural Product: NPC114692

Natural Product IDNPC114692
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
VQTMNYUOKHAJED-RULIEQGVSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 101035653
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0002049] Terpene glycosides
          • [CHEMONTID:0001580] Triterpene glycosides
            • [CHEMONTID:0002358] Triterpene saponins

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 VQTMNYUOKHAJED-RULIEQGVSA-N
Standard InCHI InChI=1S/C54H88O23/c1-22-31(58)34(61)39(66)45(70-22)76-42-36(63)33(60)26(20-56)72-47(42)77-43-38(65)37(64)41(44(68)69)75-48(43)73-29-12-13-51(5)27(52(29,6)21-57)11-14-54(8)28(51)10-9-23-24-17-49(2,3)18-30(50(24,4)15-16-53(23,54)7)74-46-40(67)35(62)32(59)25(19-55)71-46/h9,22,24-43,45-48,55-67H,10-21H2,1-8H3,(H,68,69)/t22-,24-,25+,26+,27+,28+,29-,30+,31-,32+,33-,34+,35-,36-,37-,38-,39+,40+,41-,42+,43+,45-,46-,47-,48+,50+,51-,52+,53+,54+/m0/s1
SMILES C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)O[C@@H]1[C@H]([C@H]([C@@H](CO)O[C@H]1O[C@@H]1[C@H]([C@@H]([C@@H](C(=O)O)O[C@H]1O[C@H]1CC[C@@]2(C)[C@@H](CC[C@]3(C)[C@@H]2CC=C2[C@@H]4CC(C)(C)C[C@H]([C@]4(C)CC[C@@]32C)O[C@H]2[C@@H]([C@H]([C@@H]([C@@H](CO)O2)O)O)O)[C@@]1(C)CO)O)O)O)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1104.57 Volume:   1062.434
?
Van der Waals volume.
Dense:   1.04 LogP:   0.036
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.228
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.215
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   12.0 Rigid Bonds:   51.0
TPSA:   374.13
?
Topological Polar Surface Area.
H-Bond Acceptor:   23.0
H-Bond Donor:   14.0 Rings:   9.0
Heavy Atoms:   23.0

MedChem Properties

QED Drug-Likeness Score:   0.078 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   6.893 Fsp3:   0.944
MCE-18:   198.857
?
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:   0.692 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.005
?
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:   0.338 Promiscuous compounds:   0.155

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.435 MDCK Permeability:   -5.051
Pgp-inhibitor:   0.0 Pgp-substrate:   0.128
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):   0.987
20% Bioavailability (F20%):   0.866 30% Bioavailability (F30%):   0.999
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.253
Plasma Protein Binding (PPB):   62.681% Volume Distribution (VD):   -0.396
Fu: 23.003%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   0.999 BCRP inhibitor:   0.0
BSEP inhibitor:   0.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.001 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:   0.001
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):  -0.494 Half-life (T1/2):  4.026

ADMET: Toxicity

hERG Blockers:  0.001 hERG Blockers (10um):  0.003
Human Hepatotoxicity (H-HT):  0.594 Drug-induced Liver Injury (DILI):  0.986
AMES Toxicity:  0.939 Rat Oral Acute Toxicity:  0.003
Maximum Recommended Daily Dose:  0.0 Skin Sensitization:  1.0
Carcinogencity:  0.035 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.001
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.761 Drug-induced Nephrotoxicity:  0.997
Genotoxicity:  0.706 RPMI-8226 Immunitoxicity:  0.263
A549 Cytotoxicity:  0.927 Hek293 Cytotoxicity:  0.512
BCF:   1.004
?
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:   3.41
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.847
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   3.821
?
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
NPO20620 Eucalyptus cypellocarpa Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[11000030]
NPO18462 Calliactis parasitica Species Hormathiidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19033 Sargassum lacerifolium Species Sargassaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18125 Suillus variegatus Species Suillaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17542 Aconitum orientale Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20277 Pentzia eenii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15338 Lampranthus aurantiacus Species Aizoaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO17315 Ceanothus integerrimus Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO20620 Eucalyptus cypellocarpa Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24375 Micrococcus luteus Species Micrococcaceae Bacteria n.a. n.a. n.a. Database[COCONUT]
NPO17315 Ceanothus integerrimus Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17542 Aconitum orientale Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17542 Aconitum orientale Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20620 Eucalyptus cypellocarpa Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17315 Ceanothus integerrimus Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12227 Xylopia acutiflora Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24375 Micrococcus luteus Species Micrococcaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO19033 Sargassum lacerifolium Species Sargassaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17542 Aconitum orientale Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17315 Ceanothus integerrimus Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20620 Eucalyptus cypellocarpa Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18462 Calliactis parasitica Species Hormathiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20346 Acacia retinoides Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19504 Solanum canense Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO25819.1 Gueldenstaedtia verna subsp. multiflora Subspecies Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20277 Pentzia eenii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18125 Suillus variegatus Species Suillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15338 Lampranthus aurantiacus Species Aizoaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23977 Helichrysum moeserianum Species Asteraceae 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
NPT1135 Cell line Hepatocyte Rattus norvegicus Activity = 0.0 % PMID[29353722]

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 NPC114692 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
0.9891 High Similarity NPC95437
0.9783 High Similarity NPC131469
0.9 High Similarity NPC313110
0.86 High Similarity NPC187618
0.84 Intermediate Similarity NPC236657
0.81 Intermediate Similarity NPC118440
0.8058 Intermediate Similarity NPC120116
0.713 Intermediate Similarity NPC218954
0.6635 Remote Similarity NPC12288
0.6514 Remote Similarity NPC251768
0.6306 Remote Similarity NPC482722
0.6306 Remote Similarity NPC471963
0.6306 Remote Similarity NPC162574
0.6296 Remote Similarity NPC472949
0.6281 Remote Similarity NPC484061
0.6281 Remote Similarity NPC484062
0.6204 Remote Similarity NPC482748
0.6147 Remote Similarity NPC473884
0.6129 Remote Similarity NPC484059
0.6129 Remote Similarity NPC484060
0.6111 Remote Similarity NPC25605
0.6087 Remote Similarity NPC301449
0.6087 Remote Similarity NPC601290
0.6053 Remote Similarity NPC64715
0.6053 Remote Similarity NPC302887
0.6048 Remote Similarity NPC258617
0.595 Remote Similarity NPC482736
0.595 Remote Similarity NPC482738
0.5948 Remote Similarity NPC477075
0.5938 Remote Similarity NPC484063
0.5938 Remote Similarity NPC484064
0.5865 Remote Similarity NPC224121
0.5854 Remote Similarity NPC277212
0.5854 Remote Similarity NPC30279
0.5833 Remote Similarity NPC164194
0.5812 Remote Similarity NPC486564
0.5763 Remote Similarity NPC160452
0.5752 Remote Similarity NPC192791
0.575 Remote Similarity NPC471962
0.5739 Remote Similarity NPC139044
0.568 Remote Similarity NPC82380
0.568 Remote Similarity NPC244296
0.5669 Remote Similarity NPC225791
0.5664 Remote Similarity NPC475171
0.5652 Remote Similarity NPC11551
0.56 Remote Similarity NPC47995
0.5593 Remote Similarity NPC114484
0.5577 Remote Similarity NPC204407
0.5575 Remote Similarity NPC157868
0.5565 Remote Similarity NPC114304
0.5546 Remote Similarity NPC23275
0.5546 Remote Similarity NPC477076
0.5546 Remote Similarity NPC477079
0.5538 Remote Similarity NPC11577
0.5538 Remote Similarity NPC141600
0.5536 Remote Similarity NPC174679
0.5536 Remote Similarity NPC279554
0.5536 Remote Similarity NPC309780
0.5536 Remote Similarity NPC59804
0.5524 Remote Similarity NPC57362
0.552 Remote Similarity NPC471550
0.5517 Remote Similarity NPC148603
0.5508 Remote Similarity NPC486563
0.5478 Remote Similarity NPC242840
0.5424 Remote Similarity NPC475504
0.541 Remote Similarity NPC480939
0.541 Remote Similarity NPC480936
0.5403 Remote Similarity NPC151543
0.5391 Remote Similarity NPC469946
0.5372 Remote Similarity NPC477077
0.5372 Remote Similarity NPC477078
0.5366 Remote Similarity NPC472267
0.5366 Remote Similarity NPC115656
0.5354 Remote Similarity NPC46823
0.5345 Remote Similarity NPC112352
0.5339 Remote Similarity NPC475591
0.5339 Remote Similarity NPC236870
0.5333 Remote Similarity NPC276093
0.5328 Remote Similarity NPC469947
0.5328 Remote Similarity NPC480948
0.531 Remote Similarity NPC136877
0.5304 Remote Similarity NPC488561
0.5294 Remote Similarity NPC257468
0.5294 Remote Similarity NPC123796
0.5289 Remote Similarity NPC482737
0.5289 Remote Similarity NPC481079
0.5289 Remote Similarity NPC482735
0.5276 Remote Similarity NPC269484
0.5276 Remote Similarity NPC470218
0.5276 Remote Similarity NPC97918
0.5271 Remote Similarity NPC470518
0.5271 Remote Similarity NPC21691
0.5268 Remote Similarity NPC270667
0.5254 Remote Similarity NPC159309
0.5254 Remote Similarity NPC173859
0.5254 Remote Similarity NPC86222
0.5246 Remote Similarity NPC470477
0.5242 Remote Similarity NPC107536
0.5242 Remote Similarity NPC280029
0.5242 Remote Similarity NPC9470
0.5231 Remote Similarity NPC265841
0.5231 Remote Similarity NPC476774
0.521 Remote Similarity NPC471383
0.5203 Remote Similarity NPC187290
0.52 Remote Similarity NPC252657
0.52 Remote Similarity NPC88311
0.5164 Remote Similarity NPC323359
0.5152 Remote Similarity NPC476779
0.5128 Remote Similarity NPC22956
0.5126 Remote Similarity NPC40775
0.5126 Remote Similarity NPC44716
0.5126 Remote Similarity NPC480475
0.5124 Remote Similarity NPC482755
0.5118 Remote Similarity NPC323341
0.5116 Remote Similarity NPC252289
0.5116 Remote Similarity NPC305793
0.5115 Remote Similarity NPC476780
0.5093 Remote Similarity NPC606107
0.5086 Remote Similarity NPC127056
0.5085 Remote Similarity NPC75417
0.5079 Remote Similarity NPC76972
0.5079 Remote Similarity NPC469782
0.5079 Remote Similarity NPC204414
0.5079 Remote Similarity NPC610204
0.5043 Remote Similarity NPC295371
0.5043 Remote Similarity NPC482751
0.5042 Remote Similarity NPC309714
0.5042 Remote Similarity NPC605226
0.5041 Remote Similarity NPC31193
0.504 Remote Similarity NPC470915
0.5039 Remote Similarity NPC123522
0.5039 Remote Similarity NPC283417
0.5039 Remote Similarity NPC100639
0.5039 Remote Similarity NPC200049
0.5038 Remote Similarity NPC65105
0.5037 Remote Similarity NPC476775
0.5034 Remote Similarity NPC124828

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC114692 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