Natural Product: NPC44802

Natural Product IDNPC44802
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
YRJVEPWBEBAMTP-ALIOCGAUSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 101942167
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 YRJVEPWBEBAMTP-ALIOCGAUSA-N
Standard InCHI InChI=1S/C54H86O25/c1-49-13-14-50(2,48(71)79-46-40(68)35(63)32(60)26(75-46)20-72-44-38(66)33(61)30(58)24(18-55)73-44)17-23(49)22-7-8-28-51(3)11-10-29(52(4,21-57)27(51)9-12-54(28,6)53(22,5)16-15-49)76-47-42(37(65)36(64)41(77-47)43(69)70)78-45-39(67)34(62)31(59)25(19-56)74-45/h7,23-42,44-47,55-68H,8-21H2,1-6H3,(H,69,70)/t23-,24+,25+,26+,27+,28+,29-,30+,31+,32+,33-,34-,35-,36-,37-,38+,39+,40+,41-,42+,44+,45-,46-,47+,49+,50+,51-,52+,53+,54+/m0/s1
SMILES C[C@@]12CC[C@](C)(C[C@H]2C2=CC[C@@H]3[C@@]4(C)CC[C@@H]([C@](C)(CO)[C@@H]4CC[C@@]3(C)[C@]2(C)CC1)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](C(=O)O)O1)O)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)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](CO)O2)O)O)O)O1)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1134.55 Volume:   1077.378
?
Van der Waals volume.
Dense:   1.053 LogP:   -0.254
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.235
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.471
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   14.0 Rigid Bonds:   52.0
TPSA:   411.43
?
Topological Polar Surface Area.
H-Bond Acceptor:   25.0
H-Bond Donor:   15.0 Rings:   9.0
Heavy Atoms:   25.0

MedChem Properties

QED Drug-Likeness Score:   0.05 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   6.954 Fsp3:   0.926
MCE-18:   199.385
?
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:   0.676 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.008
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.001
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.259 Promiscuous compounds:   0.106

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -7.013 MDCK Permeability:   -4.866
Pgp-inhibitor:   0.0 Pgp-substrate:   0.901
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):   0.62
20% Bioavailability (F20%):   0.74 30% Bioavailability (F30%):   0.999
50% Bioavailability (F50%):   0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.002 MRP1:   0.976
Plasma Protein Binding (PPB):   58.194% Volume Distribution (VD):   -0.36
Fu: 27.851%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   0.997 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:   0.002
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):  -0.699 Half-life (T1/2):  4.366

ADMET: Toxicity

hERG Blockers:  0.0 hERG Blockers (10um):  0.0
Human Hepatotoxicity (H-HT):  0.711 Drug-induced Liver Injury (DILI):  0.987
AMES Toxicity:  0.949 Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.0 Skin Sensitization:  1.0
Carcinogencity:  0.041 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.613 Drug-induced Nephrotoxicity:  1.0
Genotoxicity:  0.892 RPMI-8226 Immunitoxicity:  0.19
A549 Cytotoxicity:  0.689 Hek293 Cytotoxicity:  0.163
BCF:   0.552
?
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:   3.265
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.705
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   3.722
?
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
NPO29532 Vigna angularis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3734 Vigna umbellata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO18224 Vigna umbeuata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO29532 Vigna angularis Species Fabaceae Eukaryota Leaf Diffusate n.a. n.a. Database[FooDB]
NPO29532 Vigna angularis Species Fabaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO29532 Vigna angularis Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO29532 Vigna angularis Species Fabaceae Eukaryota n.a. n.a. Database[FooDB]
NPO29532 Vigna angularis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29532 Vigna angularis Species Fabaceae Eukaryota Seeds n.a. Database[Phenol-Explorer]
NPO29532 Vigna angularis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3734 Vigna umbellata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29532 Vigna angularis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18224 Vigna umbeuata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO29532 Vigna angularis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3734 Vigna umbellata 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

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 NPC44802 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
0.7075 Intermediate Similarity NPC251768
0.6949 Remote Similarity NPC258617
0.6923 Remote Similarity NPC473373
0.6822 Remote Similarity NPC309714
0.6757 Remote Similarity NPC301449
0.6757 Remote Similarity NPC601290
0.6697 Remote Similarity NPC118440
0.6696 Remote Similarity NPC187618
0.6667 Remote Similarity NPC247315
0.6667 Remote Similarity NPC482728
0.6667 Remote Similarity NPC470218
0.6577 Remote Similarity NPC64715
0.6542 Remote Similarity NPC473884
0.6518 Remote Similarity NPC114692
0.6486 Remote Similarity NPC131469
0.6455 Remote Similarity NPC11551
0.6449 Remote Similarity NPC482748
0.6429 Remote Similarity NPC95437
0.6404 Remote Similarity NPC120116
0.6389 Remote Similarity NPC295371
0.6372 Remote Similarity NPC236657
0.633 Remote Similarity NPC473343
0.6325 Remote Similarity NPC313110
0.6273 Remote Similarity NPC192791
0.625 Remote Similarity NPC63159
0.6182 Remote Similarity NPC475171
0.6174 Remote Similarity NPC218954
0.6168 Remote Similarity NPC48499
0.6091 Remote Similarity NPC472949
0.5963 Remote Similarity NPC136877
0.5946 Remote Similarity NPC157868
0.5929 Remote Similarity NPC109588
0.5917 Remote Similarity NPC76972
0.5917 Remote Similarity NPC469782
0.5917 Remote Similarity NPC204414
0.5887 Remote Similarity NPC82380
0.5887 Remote Similarity NPC244296
0.5854 Remote Similarity NPC100639
0.5841 Remote Similarity NPC242840
0.5827 Remote Similarity NPC65105
0.5826 Remote Similarity NPC475591
0.5826 Remote Similarity NPC236870
0.5798 Remote Similarity NPC187290
0.578 Remote Similarity NPC29069
0.5776 Remote Similarity NPC31193
0.5766 Remote Similarity NPC309780
0.5739 Remote Similarity NPC473383
0.5738 Remote Similarity NPC79643
0.5736 Remote Similarity NPC298034
0.5736 Remote Similarity NPC71065
0.5736 Remote Similarity NPC11577
0.5736 Remote Similarity NPC141600
0.569 Remote Similarity NPC139044
0.5664 Remote Similarity NPC470512
0.5645 Remote Similarity NPC135904
0.5625 Remote Similarity NPC139894
0.5625 Remote Similarity NPC59804
0.5603 Remote Similarity NPC159309
0.5603 Remote Similarity NPC86222
0.56 Remote Similarity NPC283417
0.56 Remote Similarity NPC200049
0.5583 Remote Similarity NPC241909
0.5581 Remote Similarity NPC293330
0.5565 Remote Similarity NPC75417
0.5556 Remote Similarity NPC256798
0.5528 Remote Similarity NPC252657
0.5528 Remote Similarity NPC88311
0.552 Remote Similarity NPC155410
0.552 Remote Similarity NPC123199
0.5508 Remote Similarity NPC470514
0.5508 Remote Similarity NPC222580
0.5478 Remote Similarity NPC471547
0.5478 Remote Similarity NPC469946
0.5476 Remote Similarity NPC471550
0.547 Remote Similarity NPC40775
0.547 Remote Similarity NPC173859
0.547 Remote Similarity NPC148603
0.5469 Remote Similarity NPC470518
0.5455 Remote Similarity NPC480474
0.5447 Remote Similarity NPC472267
0.5447 Remote Similarity NPC107536
0.5447 Remote Similarity NPC115656
0.5447 Remote Similarity NPC280029
0.5447 Remote Similarity NPC9470
0.5431 Remote Similarity NPC112352
0.5426 Remote Similarity NPC476774
0.5426 Remote Similarity NPC476780
0.542 Remote Similarity NPC202828
0.542 Remote Similarity NPC119592
0.5417 Remote Similarity NPC114484
0.5403 Remote Similarity NPC60557
0.5403 Remote Similarity NPC67857
0.5385 Remote Similarity NPC471548
0.5385 Remote Similarity NPC41061
0.5385 Remote Similarity NPC227551
0.5378 Remote Similarity NPC475504
0.5378 Remote Similarity NPC470513
0.5378 Remote Similarity NPC297263
0.5372 Remote Similarity NPC481079
0.537 Remote Similarity NPC224121
0.536 Remote Similarity NPC192600
0.5354 Remote Similarity NPC269484
0.5354 Remote Similarity NPC97918
0.5344 Remote Similarity NPC43550
0.5339 Remote Similarity NPC473401
0.5339 Remote Similarity NPC480475
0.5328 Remote Similarity NPC480473
0.5323 Remote Similarity NPC185466
0.5317 Remote Similarity NPC284449
0.5317 Remote Similarity NPC323341
0.5312 Remote Similarity NPC252289
0.5312 Remote Similarity NPC305793
0.5303 Remote Similarity NPC305981
0.5299 Remote Similarity NPC482741
0.5299 Remote Similarity NPC482745
0.5299 Remote Similarity NPC482743
0.5299 Remote Similarity NPC146753
0.5294 Remote Similarity NPC148417
0.5289 Remote Similarity NPC281148
0.5285 Remote Similarity NPC31838
0.5271 Remote Similarity NPC329923
0.5271 Remote Similarity NPC475281
0.5271 Remote Similarity NPC4749
0.5268 Remote Similarity NPC189884
0.5268 Remote Similarity NPC90856
0.5268 Remote Similarity NPC138334
0.5263 Remote Similarity NPC261506
0.5263 Remote Similarity NPC4328
0.5263 Remote Similarity NPC12288
0.5259 Remote Similarity NPC482751
0.525 Remote Similarity NPC257468
0.5246 Remote Similarity NPC323359
0.5234 Remote Similarity NPC204407
0.5231 Remote Similarity NPC21691
0.5225 Remote Similarity NPC209894
0.5224 Remote Similarity NPC476775
0.521 Remote Similarity NPC305267
0.521 Remote Similarity NPC473459
0.5207 Remote Similarity NPC302887
0.5203 Remote Similarity NPC485563
0.5197 Remote Similarity NPC165204
0.5194 Remote Similarity NPC25663
0.5185 Remote Similarity NPC57362
0.5172 Remote Similarity NPC150400
0.5172 Remote Similarity NPC127056
0.5167 Remote Similarity NPC471383
0.5167 Remote Similarity NPC162574
0.5164 Remote Similarity NPC276093
0.5156 Remote Similarity NPC219180
0.5147 Remote Similarity NPC250247
0.5133 Remote Similarity NPC214484
0.5128 Remote Similarity NPC39211
0.5126 Remote Similarity NPC104071
0.5124 Remote Similarity NPC609763
0.5122 Remote Similarity NPC482737
0.5122 Remote Similarity NPC477075
0.5122 Remote Similarity NPC477076
0.5122 Remote Similarity NPC477079
0.512 Remote Similarity NPC11242
0.512 Remote Similarity NPC470915
0.5116 Remote Similarity NPC475160
0.5116 Remote Similarity NPC475140
0.5116 Remote Similarity NPC191827
0.5116 Remote Similarity NPC473714
0.5088 Remote Similarity NPC164194
0.5086 Remote Similarity NPC174679
0.5086 Remote Similarity NPC279554
0.5086 Remote Similarity NPC482750
0.5083 Remote Similarity NPC102439
0.5082 Remote Similarity NPC119794
0.5081 Remote Similarity NPC488564
0.5081 Remote Similarity NPC295823
0.5081 Remote Similarity NPC174720
0.5081 Remote Similarity NPC160452
0.5081 Remote Similarity NPC475467
0.5081 Remote Similarity NPC477077
0.5081 Remote Similarity NPC477078
0.5076 Remote Similarity NPC265841
0.5076 Remote Similarity NPC488308
0.5075 Remote Similarity NPC481081
0.5047 Remote Similarity NPC167383
0.5041 Remote Similarity NPC470515
0.5041 Remote Similarity NPC482740
0.504 Remote Similarity NPC481078
0.5038 Remote Similarity NPC271610
0.5038 Remote Similarity NPC312650
0.5038 Remote Similarity NPC481080
0.5037 Remote Similarity NPC302543

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC44802 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