Natural Product: NPC482010

Natural Product IDNPC482010
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
MEOJUIFNOCVHMQ-FQUVNWGASA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 11535483
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 MEOJUIFNOCVHMQ-FQUVNWGASA-N
Standard InCHI InChI=1S/C59H95NO26/c1-25(63)60-36-44(84-49-43(73)38(68)29(65)21-78-49)40(70)31(22-79-48-42(72)37(67)28(64)20-77-48)82-47(36)83-35-12-13-55(6)32(54(35,4)5)11-14-56(7)33(55)10-9-26-27-17-53(2,3)15-16-59(27,34(66)18-57(26,56)8)52(75)86-50-45(41(71)39(69)30(19-61)81-50)85-51-46(74)58(76,23-62)24-80-51/h9,27-51,61-62,64-74,76H,10-24H2,1-8H3,(H,60,63)/t27-,28-,29+,30+,31+,32-,33+,34+,35-,36+,37-,38-,39+,40+,41-,42+,43+,44+,45+,46-,47-,48-,49-,50-,51-,55-,56+,57+,58+,59+/m0/s1
SMILES CC(=N[C@@H]1[C@H]([C@@H]([C@@H](CO[C@H]2[C@@H]([C@H]([C@H](CO2)O)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)CC[C@@]4([C@@H](C[C@@]32C)O)C(=O)O[C@H]2[C@@H]([C@H]([C@@H]([C@@H](CO)O2)O)O)O[C@H]2[C@@H]([C@@](CO)(CO2)O)O)C1(C)C)O)O[C@H]1[C@@H]([C@H]([C@@H](CO1)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1233.61 Volume:   1175.088
?
Van der Waals volume.
Dense:   1.05 LogP:   0.282
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.061
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.268
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   15.0 Rigid Bonds:   57.0
TPSA:   425.18
?
Topological Polar Surface Area.
H-Bond Acceptor:   27.0
H-Bond Donor:   15.0 Rings:   10.0
Heavy Atoms:   27.0

MedChem Properties

QED Drug-Likeness Score:   0.028 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.471 Fsp3:   0.932
MCE-18:   218.982
?
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:   0.727 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:   0.067 Promiscuous compounds:   0.292

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.481 MDCK Permeability:   -5.066
Pgp-inhibitor:   0.0 Pgp-substrate:   0.837
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):   0.963
20% Bioavailability (F20%):   0.885 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.007 MRP1:   0.004
Plasma Protein Binding (PPB):   62.125% Volume Distribution (VD):   -0.375
Fu: 25.219%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.003
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:   0.98 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.246
HLM stability:   0.953
?
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):  -0.446 Half-life (T1/2):  3.5

ADMET: Toxicity

hERG Blockers:  0.001 hERG Blockers (10um):  0.002
Human Hepatotoxicity (H-HT):  0.995 Drug-induced Liver Injury (DILI):  0.99
AMES Toxicity:  0.994 Rat Oral Acute Toxicity:  0.001
Maximum Recommended Daily Dose:  0.001 Skin Sensitization:  1.0
Carcinogencity:  0.109 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.001
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.655 Drug-induced Nephrotoxicity:  0.992
Genotoxicity:  0.966 RPMI-8226 Immunitoxicity:  0.27
A549 Cytotoxicity:  0.959 Hek293 Cytotoxicity:  0.682
BCF:   0.856
?
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:   3.726
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.751
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.572
?
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
NPO12551 Entada pursaetha Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[16124758]
NPO12551 Entada pursaetha Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12551 Entada pursaetha Species Fabaceae 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
NPT393 Cell line HCT-116 Homo sapiens IC50 > 100.0 ug.mL-1 PMID[16124758]
NPT139 Cell line HT-29 Homo sapiens IC50 > 100.0 ug.mL-1 PMID[16124758]

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 NPC482010 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
0.8667 High Similarity NPC482011
0.8049 Intermediate Similarity NPC482012
0.6972 Remote Similarity NPC475584
0.6972 Remote Similarity NPC475152
0.6746 Remote Similarity NPC123522
0.6591 Remote Similarity NPC470876
0.6449 Remote Similarity NPC489209
0.6429 Remote Similarity NPC104137
0.6429 Remote Similarity NPC26626
0.6408 Remote Similarity NPC489208
0.6286 Remote Similarity NPC8524
0.625 Remote Similarity NPC476113
0.6241 Remote Similarity NPC33012
0.6186 Remote Similarity NPC1046
0.6149 Remote Similarity NPC475394
0.6129 Remote Similarity NPC164389
0.609 Remote Similarity NPC283417
0.609 Remote Similarity NPC200049
0.6087 Remote Similarity NPC309223
0.6 Remote Similarity NPC85154
0.5954 Remote Similarity NPC172365
0.5923 Remote Similarity NPC207738
0.5912 Remote Similarity NPC13998
0.5912 Remote Similarity NPC286457
0.5891 Remote Similarity NPC481079
0.5887 Remote Similarity NPC220160
0.5887 Remote Similarity NPC469946
0.5878 Remote Similarity NPC210729
0.5878 Remote Similarity NPC82931
0.5873 Remote Similarity NPC488526
0.5859 Remote Similarity NPC64715
0.585 Remote Similarity NPC475177
0.5804 Remote Similarity NPC102505
0.5804 Remote Similarity NPC488514
0.5789 Remote Similarity NPC475892
0.5789 Remote Similarity NPC610204
0.5767 Remote Similarity NPC475527
0.5766 Remote Similarity NPC4749
0.5745 Remote Similarity NPC302543
0.5714 Remote Similarity NPC185466
0.5705 Remote Similarity NPC488618
0.5669 Remote Similarity NPC30289
0.5662 Remote Similarity NPC603137
0.5646 Remote Similarity NPC480421
0.5639 Remote Similarity NPC11242
0.5634 Remote Similarity NPC144644
0.5634 Remote Similarity NPC170407
0.56 Remote Similarity NPC480420
0.5597 Remote Similarity NPC113620
0.5592 Remote Similarity NPC329893
0.5586 Remote Similarity NPC68767
0.557 Remote Similarity NPC23020
0.557 Remote Similarity NPC488619
0.5548 Remote Similarity NPC153673
0.5528 Remote Similarity NPC100612
0.5524 Remote Similarity NPC37860
0.5522 Remote Similarity NPC815
0.5504 Remote Similarity NPC305267
0.5494 Remote Similarity NPC488620
0.5489 Remote Similarity NPC69811
0.5479 Remote Similarity NPC293031
0.5462 Remote Similarity NPC105800
0.5461 Remote Similarity NPC473645
0.5461 Remote Similarity NPC473452
0.5448 Remote Similarity NPC31838
0.5448 Remote Similarity NPC142151
0.5442 Remote Similarity NPC110385
0.5442 Remote Similarity NPC51099
0.5441 Remote Similarity NPC610461
0.5436 Remote Similarity NPC275225
0.5426 Remote Similarity NPC117714
0.5425 Remote Similarity NPC484831
0.5425 Remote Similarity NPC484830
0.542 Remote Similarity NPC297263
0.5414 Remote Similarity NPC606145
0.5396 Remote Similarity NPC475140
0.5394 Remote Similarity NPC265699
0.5391 Remote Similarity NPC213674
0.539 Remote Similarity NPC21691
0.5385 Remote Similarity NPC232237
0.5379 Remote Similarity NPC70809
0.5375 Remote Similarity NPC475444
0.5375 Remote Similarity NPC473679
0.5352 Remote Similarity NPC480418
0.535 Remote Similarity NPC300655
0.535 Remote Similarity NPC13989
0.535 Remote Similarity NPC196874
0.5344 Remote Similarity NPC63159
0.5342 Remote Similarity NPC267694
0.5333 Remote Similarity NPC609281
0.5328 Remote Similarity NPC607904
0.5325 Remote Similarity NPC174336
0.5324 Remote Similarity NPC123199
0.5315 Remote Similarity NPC475514
0.5302 Remote Similarity NPC480422
0.5301 Remote Similarity NPC475599
0.5299 Remote Similarity NPC301449
0.5299 Remote Similarity NPC601290
0.5286 Remote Similarity NPC480423
0.5282 Remote Similarity NPC473386
0.5276 Remote Similarity NPC472270
0.5276 Remote Similarity NPC112492
0.5259 Remote Similarity NPC160452
0.525 Remote Similarity NPC478559
0.525 Remote Similarity NPC478560
0.5248 Remote Similarity NPC471577
0.5223 Remote Similarity NPC484829
0.5221 Remote Similarity NPC481078
0.5217 Remote Similarity NPC222951
0.5203 Remote Similarity NPC250247
0.5202 Remote Similarity NPC187497
0.5196 Remote Similarity NPC475649
0.5194 Remote Similarity NPC488561
0.519 Remote Similarity NPC233223
0.519 Remote Similarity NPC183816
0.519 Remote Similarity NPC43589
0.5188 Remote Similarity NPC123796
0.5185 Remote Similarity NPC291903
0.5185 Remote Similarity NPC75318
0.5175 Remote Similarity NPC57484
0.5154 Remote Similarity NPC263756
0.5149 Remote Similarity NPC302887
0.5127 Remote Similarity NPC329878
0.5109 Remote Similarity NPC475345
0.5109 Remote Similarity NPC187290
0.5106 Remote Similarity NPC135904
0.5072 Remote Similarity NPC606553
0.5071 Remote Similarity NPC79643
0.5062 Remote Similarity NPC311178
0.5061 Remote Similarity NPC482013
0.5038 Remote Similarity NPC76497
0.5036 Remote Similarity NPC295823
0.5036 Remote Similarity NPC174720
0.5036 Remote Similarity NPC475467
0.5036 Remote Similarity NPC288205
0.5036 Remote Similarity NPC51465
0.5035 Remote Similarity NPC25663
0.5035 Remote Similarity NPC243680
0.5034 Remote Similarity NPC265841
0.5034 Remote Similarity NPC236638
0.5034 Remote Similarity NPC294453
0.5034 Remote Similarity NPC481081
0.503 Remote Similarity NPC322904

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC482010 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