Natural Product: NPC484061

Natural Product IDNPC484061
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
DMEKIQJMBMEDLM-BBZHSQTRSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 44566321
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 DMEKIQJMBMEDLM-BBZHSQTRSA-N
Standard InCHI InChI=1S/C67H106O30/c1-13-26(2)56(85)91-37-21-62(6,7)20-31-30-14-15-35-64(10)18-17-36(63(8,9)34(64)16-19-65(35,11)66(30,12)22-38(88-29(5)71)67(31,37)25-70)92-61-54(97-58-48(81)44(77)41(74)32(23-68)89-58)50(49(82)51(94-61)55(83)84)93-60-53(46(79)42(75)33(24-69)90-60)96-59-52(45(78)40(73)28(4)87-59)95-57-47(80)43(76)39(72)27(3)86-57/h13-14,27-28,31-54,57-61,68-70,72-82H,15-25H2,1-12H3,(H,83,84)/b26-13+/t27-,28-,31-,32+,33+,34-,35+,36-,37-,38+,39-,40-,41-,42-,43+,44-,45+,46-,47+,48+,49-,50-,51-,52+,53+,54+,57-,58-,59-,60-,61+,64-,65+,66+,67+/m0/s1
SMILES C/C=C(C)/C(=O)O[C@H]1CC(C)(C)C[C@H]2C3=CC[C@@H]4[C@@]5(C)CC[C@@H](C(C)(C)[C@@H]5CC[C@@]4(C)[C@]3(C)C[C@H]([C@@]12CO)OC(=O)C)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](C)O1)O)O)O[C@H]1[C@@H]([C@@H]([C@H]([C@H](C)O1)O)O)O)O[C@H]1[C@@H]([C@H]([C@H]([C@@H](CO)O1)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1390.68 Volume:   1332.347
?
Van der Waals volume.
Dense:   1.044 LogP:   0.366
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.504
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.711
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   19.0 Rigid Bonds:   60.0
TPSA:   465.42
?
Topological Polar Surface Area.
H-Bond Acceptor:   30.0
H-Bond Donor:   15.0 Rings:   10.0
Heavy Atoms:   30.0

MedChem Properties

QED Drug-Likeness Score:   0.034 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.792 Fsp3:   0.896
MCE-18:   227.528
?
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:   0.862 Fluc inhibitor:   0.002
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.001
?
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:   0.384 Promiscuous compounds:   0.259

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.218 MDCK Permeability:   -5.144
Pgp-inhibitor:   0.0 Pgp-substrate:   0.98
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):   0.999
20% Bioavailability (F20%):   0.998 30% Bioavailability (F30%):   0.999
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.987
Plasma Protein Binding (PPB):   60.219% Volume Distribution (VD):   -0.46
Fu: 22.056%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   0.998
OATP1B3 inhibitor:   0.1 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:   0.261
HLM stability:   0.004
?
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):  -0.7 Half-life (T1/2):  3.684

ADMET: Toxicity

hERG Blockers:  0.0 hERG Blockers (10um):  0.001
Human Hepatotoxicity (H-HT):  0.617 Drug-induced Liver Injury (DILI):  0.994
AMES Toxicity:  0.99 Rat Oral Acute Toxicity:  0.002
Maximum Recommended Daily Dose:  0.0 Skin Sensitization:  1.0
Carcinogencity:  0.011 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.944 Drug-induced Nephrotoxicity:  0.999
Genotoxicity:  0.893 RPMI-8226 Immunitoxicity:  0.318
A549 Cytotoxicity:  0.953 Hek293 Cytotoxicity:  0.347
BCF:   0.199
?
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:   3.508
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.65
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.324
?
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
NPO40886 Mmaesa laxiflora Species n.a. n.a. n.a. n.a. n.a. PMID[10395506]

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
NPT2 Others Unspecified n.a. Activity = 41.0 % PMID[10395506]

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 NPC484061 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
1.0 High Similarity NPC484062
0.8684 High Similarity NPC484059
0.8684 High Similarity NPC484060
0.8407 Intermediate Similarity NPC277212
0.8407 Intermediate Similarity NPC30279
0.75 Intermediate Similarity NPC484063
0.75 Intermediate Similarity NPC484064
0.7479 Intermediate Similarity NPC47995
0.7479 Intermediate Similarity NPC46823
0.7333 Intermediate Similarity NPC473918
0.7236 Intermediate Similarity NPC225791
0.7193 Intermediate Similarity NPC302887
0.7154 Intermediate Similarity NPC265841
0.7131 Intermediate Similarity NPC71391
0.7009 Intermediate Similarity NPC160452
0.6639 Remote Similarity NPC609119
0.6581 Remote Similarity NPC475591
0.6581 Remote Similarity NPC236870
0.6562 Remote Similarity NPC271610
0.6557 Remote Similarity NPC25998
0.6512 Remote Similarity NPC476779
0.6475 Remote Similarity NPC480939
0.6475 Remote Similarity NPC605294
0.6429 Remote Similarity NPC283417
0.6429 Remote Similarity NPC200049
0.6429 Remote Similarity NPC602995
0.6406 Remote Similarity NPC178264
0.6393 Remote Similarity NPC329976
0.6393 Remote Similarity NPC469947
0.6393 Remote Similarity NPC480948
0.6364 Remote Similarity NPC23275
0.6364 Remote Similarity NPC477079
0.6356 Remote Similarity NPC44716
0.6328 Remote Similarity NPC181066
0.6328 Remote Similarity NPC192765
0.6328 Remote Similarity NPC329828
0.6288 Remote Similarity NPC302543
0.6281 Remote Similarity NPC114692
0.626 Remote Similarity NPC187290
0.625 Remote Similarity NPC131469
0.624 Remote Similarity NPC313110
0.6198 Remote Similarity NPC95437
0.6107 Remote Similarity NPC476774
0.6107 Remote Similarity NPC476780
0.6098 Remote Similarity NPC477076
0.6061 Remote Similarity NPC312650
0.6048 Remote Similarity NPC477077
0.6031 Remote Similarity NPC21691
0.6 Remote Similarity NPC476775
0.6 Remote Similarity NPC605226
0.5985 Remote Similarity NPC488308
0.597 Remote Similarity NPC476777
0.5968 Remote Similarity NPC477075
0.5966 Remote Similarity NPC22956
0.5959 Remote Similarity NPC477474
0.595 Remote Similarity NPC251768
0.5935 Remote Similarity NPC64715
0.592 Remote Similarity NPC187618
0.592 Remote Similarity NPC120116
0.5891 Remote Similarity NPC477465
0.5887 Remote Similarity NPC236657
0.5882 Remote Similarity NPC603026
0.587 Remote Similarity NPC476776
0.5847 Remote Similarity NPC25605
0.5797 Remote Similarity NPC476778
0.5789 Remote Similarity NPC470518
0.5785 Remote Similarity NPC192791
0.5785 Remote Similarity NPC112352
0.5781 Remote Similarity NPC470475
0.576 Remote Similarity NPC114484
0.5748 Remote Similarity NPC477194
0.5736 Remote Similarity NPC610204
0.5725 Remote Similarity NPC488309
0.5714 Remote Similarity NPC301449
0.5714 Remote Similarity NPC477467
0.5714 Remote Similarity NPC601290
0.5704 Remote Similarity NPC258617
0.5703 Remote Similarity NPC470915
0.5691 Remote Similarity NPC164389
0.5691 Remote Similarity NPC46665
0.5676 Remote Similarity NPC477470
0.5676 Remote Similarity NPC477472
0.5645 Remote Similarity NPC118440
0.5625 Remote Similarity NPC609281
0.5597 Remote Similarity NPC4749
0.5593 Remote Similarity NPC164194
0.5574 Remote Similarity NPC469946
0.5573 Remote Similarity NPC123522
0.5547 Remote Similarity NPC477078
0.553 Remote Similarity NPC284449
0.5507 Remote Similarity NPC110700
0.5504 Remote Similarity NPC36831
0.5496 Remote Similarity NPC268184
0.5474 Remote Similarity NPC470876
0.5462 Remote Similarity NPC480936
0.5455 Remote Similarity NPC151543
0.5455 Remote Similarity NPC478155
0.5455 Remote Similarity NPC478154
0.5448 Remote Similarity NPC264566
0.544 Remote Similarity NPC159309
0.544 Remote Similarity NPC480475
0.544 Remote Similarity NPC86222
0.5426 Remote Similarity NPC470477
0.5372 Remote Similarity NPC12288
0.5368 Remote Similarity NPC82380
0.5368 Remote Similarity NPC244296
0.5366 Remote Similarity NPC472949
0.5366 Remote Similarity NPC157868
0.536 Remote Similarity NPC114304
0.5359 Remote Similarity NPC477473
0.5354 Remote Similarity NPC470913
0.5354 Remote Similarity NPC123796
0.5349 Remote Similarity NPC481079
0.5349 Remote Similarity NPC218954
0.5333 Remote Similarity NPC269484
0.5333 Remote Similarity NPC97918
0.5324 Remote Similarity NPC484833
0.5323 Remote Similarity NPC263756
0.5323 Remote Similarity NPC213674
0.5308 Remote Similarity NPC480474
0.5308 Remote Similarity NPC477192
0.5303 Remote Similarity NPC472267
0.5303 Remote Similarity NPC107536
0.5303 Remote Similarity NPC115656
0.5303 Remote Similarity NPC280029
0.5303 Remote Similarity NPC9470
0.5303 Remote Similarity NPC478152
0.5303 Remote Similarity NPC478151
0.5299 Remote Similarity NPC470911
0.5285 Remote Similarity NPC127056
0.5276 Remote Similarity NPC162574
0.5271 Remote Similarity NPC470914
0.5267 Remote Similarity NPC207738
0.5263 Remote Similarity NPC475287
0.5259 Remote Similarity NPC482736
0.5259 Remote Similarity NPC482738
0.5259 Remote Similarity NPC470476
0.5259 Remote Similarity NPC135904
0.5248 Remote Similarity NPC11577
0.5248 Remote Similarity NPC141600
0.5245 Remote Similarity NPC279915
0.5242 Remote Similarity NPC488561
0.5238 Remote Similarity NPC480947
0.5234 Remote Similarity NPC470478
0.5234 Remote Similarity NPC257468
0.5231 Remote Similarity NPC324875
0.5231 Remote Similarity NPC292677
0.5227 Remote Similarity NPC11242
0.5221 Remote Similarity NPC470218
0.5217 Remote Similarity NPC57484
0.5203 Remote Similarity NPC56713
0.5203 Remote Similarity NPC475368
0.5197 Remote Similarity NPC40775
0.5197 Remote Similarity NPC148603
0.5191 Remote Similarity NPC480473
0.5182 Remote Similarity NPC252289
0.5182 Remote Similarity NPC305793
0.518 Remote Similarity NPC286457
0.5161 Remote Similarity NPC109079
0.5161 Remote Similarity NPC477469
0.5161 Remote Similarity NPC477471
0.5156 Remote Similarity NPC63159
0.5154 Remote Similarity NPC281148
0.5152 Remote Similarity NPC481078
0.5149 Remote Similarity NPC610461
0.5147 Remote Similarity NPC478150
0.513 Remote Similarity NPC220838
0.513 Remote Similarity NPC477466
0.5118 Remote Similarity NPC160415
0.5118 Remote Similarity NPC117714
0.5118 Remote Similarity NPC30289
0.5116 Remote Similarity NPC222580
0.5116 Remote Similarity NPC475504
0.5116 Remote Similarity NPC297263
0.5115 Remote Similarity NPC486564
0.5113 Remote Similarity NPC606553
0.5111 Remote Similarity NPC79643
0.5109 Remote Similarity NPC470517
0.5097 Remote Similarity NPC300655
0.5079 Remote Similarity NPC161674
0.5079 Remote Similarity NPC80843
0.5078 Remote Similarity NPC10607
0.5077 Remote Similarity NPC79718
0.507 Remote Similarity NPC305981
0.5069 Remote Similarity NPC220160
0.5039 Remote Similarity NPC68175
0.5038 Remote Similarity NPC104137
0.5038 Remote Similarity NPC475486
0.5038 Remote Similarity NPC26626
0.5038 Remote Similarity NPC78034
0.5037 Remote Similarity NPC60557
0.5037 Remote Similarity NPC252657
0.5037 Remote Similarity NPC88311
0.5037 Remote Similarity NPC473824
0.5037 Remote Similarity NPC67857
0.5036 Remote Similarity NPC329923
0.5036 Remote Similarity NPC475281
0.5036 Remote Similarity NPC251263
0.5035 Remote Similarity NPC261506

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC484061 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