Natural Product: NPC481080

Natural Product IDNPC481080
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
CDHQYHBOEFFPFG-CBYDVUCMSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 46888053
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 CDHQYHBOEFFPFG-CBYDVUCMSA-N
Standard InCHI InChI=1S/C64H104O30/c1-25-36(68)51(93-54-45(77)40(72)32(24-85-54)89-52-44(76)37(69)28(67)22-83-52)49(81)57(86-25)92-50-30(21-66)88-55(48(80)43(50)75)91-35-12-13-61(6)33(60(35,4)5)11-14-63(8)34(61)10-9-26-27-19-59(2,3)15-17-64(27,18-16-62(26,63)7)58(82)94-56-47(79)42(74)39(71)31(90-56)23-84-53-46(78)41(73)38(70)29(20-65)87-53/h9,25,27-57,65-81H,10-24H2,1-8H3/t25-,27+,28+,29+,30+,31+,32+,33-,34+,35-,36-,37-,38+,39+,40-,41-,42-,43+,44+,45+,46+,47+,48+,49+,50+,51+,52-,53+,54-,55-,56-,57-,61-,62+,63+,64-/m0/s1
SMILES C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)O[C@@H]1[C@@H](CO)O[C@H]([C@@H]([C@H]1O)O)O[C@H]1CC[C@@]2(C)[C@@H](CC[C@]3(C)[C@@H]2CC=C2[C@H]4CC(C)(C)CC[C@@]4(CC[C@@]32C)C(=O)O[C@H]2[C@@H]([C@H]([C@@H]([C@@H](CO[C@H]3[C@@H]([C@H]([C@@H]([C@@H](CO)O3)O)O)O)O2)O)O)O)C1(C)C)O)O[C@H]1[C@@H]([C@H]([C@@H](CO1)O[C@H]1[C@@H]([C@H]([C@@H](CO1)O)O)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1352.66 Volume:   1279.812
?
Van der Waals volume.
Dense:   1.057 LogP:   0.612
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.401
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.764
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   16.0 Rigid Bonds:   63.0
TPSA:   471.74
?
Topological Polar Surface Area.
H-Bond Acceptor:   30.0
H-Bond Donor:   17.0 Rings:   11.0
Heavy Atoms:   30.0

MedChem Properties

QED Drug-Likeness Score:   0.042 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.64 Fsp3:   0.953
MCE-18:   238.0
?
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:   0.742 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.006
?
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:   0.363 Promiscuous compounds:   0.074

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -7.063 MDCK Permeability:   -5.11
Pgp-inhibitor:   0.0 Pgp-substrate:   0.143
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):   0.991
20% Bioavailability (F20%):   0.032 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.009 MRP1:   0.0
Plasma Protein Binding (PPB):   49.432% Volume Distribution (VD):   -0.255
Fu: 27.523%
?
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:   0.408 CYP3A4-substrate:   0.038
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.972
HLM stability:   0.025
?
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):  -1.271 Half-life (T1/2):  5.365

ADMET: Toxicity

hERG Blockers:  0.001 hERG Blockers (10um):  0.002
Human Hepatotoxicity (H-HT):  0.746 Drug-induced Liver Injury (DILI):  0.983
AMES Toxicity:  0.994 Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.0 Skin Sensitization:  1.0
Carcinogencity:  0.003 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.42 Drug-induced Nephrotoxicity:  0.996
Genotoxicity:  0.062 RPMI-8226 Immunitoxicity:  0.392
A549 Cytotoxicity:  0.944 Hek293 Cytotoxicity:  0.513
BCF:   1.741
?
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:   3.934
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.486
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.637
?
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
NPO2435 Cephalaria scoparia Species Caprifoliaceae Eukaryota n.a. n.a. n.a. PMID[20384364]
NPO2435 Cephalaria scoparia Species Caprifoliaceae 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
NPT1190 Organism Salmonella enterica Salmonella enterica MIC = 64.0 ug.mL-1 PMID[20384364]
NPT173 Organism Klebsiella pneumoniae Klebsiella pneumoniae MIC = 64.0 ug.mL-1 PMID[20384364]
NPT19 Organism Escherichia coli Escherichia coli MIC = 128.0 ug.mL-1 PMID[20384364]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa MIC = 64.0 ug.mL-1 PMID[20384364]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 256.0 ug.mL-1 PMID[20384364]
NPT17 Organism Staphylococcus epidermidis Staphylococcus epidermidis MIC = 128.0 ug.mL-1 PMID[20384364]
NPT175 Organism Enterococcus faecalis Enterococcus faecalis MIC = 64.0 ug.mL-1 PMID[20384364]
NPT314 Organism Bacillus cereus Bacillus cereus MIC = 16.0 ug.mL-1 PMID[20384364]

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 NPC481080 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
0.887 High Similarity NPC250247
0.8839 High Similarity NPC41061
0.8839 High Similarity NPC227551
0.8772 High Similarity NPC261506
0.8772 High Similarity NPC4328
0.8684 High Similarity NPC236638
0.8684 High Similarity NPC294453
0.8684 High Similarity NPC305981
0.8679 High Similarity NPC295823
0.8679 High Similarity NPC174720
0.8679 High Similarity NPC475467
0.8649 High Similarity NPC488560
0.8559 High Similarity NPC475160
0.8559 High Similarity NPC473714
0.8522 High Similarity NPC481081
0.8496 Intermediate Similarity NPC476068
0.8435 Intermediate Similarity NPC43550
0.8304 Intermediate Similarity NPC123199
0.8136 Intermediate Similarity NPC298034
0.8136 Intermediate Similarity NPC71065
0.8125 Intermediate Similarity NPC79643
0.8051 Intermediate Similarity NPC202828
0.8051 Intermediate Similarity NPC119592
0.8 Intermediate Similarity NPC241909
0.7982 Intermediate Similarity NPC135904
0.7815 Intermediate Similarity NPC65105
0.7768 Intermediate Similarity NPC481078
0.775 Intermediate Similarity NPC136768
0.7719 Intermediate Similarity NPC60557
0.7719 Intermediate Similarity NPC475287
0.7719 Intermediate Similarity NPC67857
0.7692 Intermediate Similarity NPC48499
0.7647 Intermediate Similarity NPC110633
0.7561 Intermediate Similarity NPC220160
0.7407 Intermediate Similarity NPC295371
0.7387 Intermediate Similarity NPC148417
0.7295 Intermediate Similarity NPC258617
0.7295 Intermediate Similarity NPC475514
0.7281 Intermediate Similarity NPC481079
0.7232 Intermediate Similarity NPC63159
0.7203 Intermediate Similarity NPC192600
0.7119 Intermediate Similarity NPC76972
0.7119 Intermediate Similarity NPC469782
0.7119 Intermediate Similarity NPC204414
0.7064 Intermediate Similarity NPC475516
0.7063 Intermediate Similarity NPC70809
0.7054 Intermediate Similarity NPC104071
0.7025 Intermediate Similarity NPC100639
0.6991 Remote Similarity NPC102439
0.6964 Remote Similarity NPC223301
0.6964 Remote Similarity NPC171544
0.696 Remote Similarity NPC293330
0.6897 Remote Similarity NPC104372
0.6875 Remote Similarity NPC224381
0.6875 Remote Similarity NPC469946
0.6875 Remote Similarity NPC469778
0.6855 Remote Similarity NPC57484
0.6831 Remote Similarity NPC469776
0.6806 Remote Similarity NPC32723
0.6803 Remote Similarity NPC155410
0.6759 Remote Similarity NPC481323
0.6757 Remote Similarity NPC235405
0.6721 Remote Similarity NPC165204
0.6697 Remote Similarity NPC90856
0.6696 Remote Similarity NPC249848
0.6696 Remote Similarity NPC473459
0.6696 Remote Similarity NPC107966
0.6667 Remote Similarity NPC135334
0.6667 Remote Similarity NPC295941
0.6667 Remote Similarity NPC112352
0.6638 Remote Similarity NPC235438
0.6622 Remote Similarity NPC481324
0.6609 Remote Similarity NPC30735
0.6583 Remote Similarity NPC187290
0.6581 Remote Similarity NPC297263
0.6486 Remote Similarity NPC29069
0.648 Remote Similarity NPC470218
0.6471 Remote Similarity NPC114484
0.6446 Remote Similarity NPC31838
0.6441 Remote Similarity NPC475504
0.6422 Remote Similarity NPC128925
0.6418 Remote Similarity NPC480422
0.6417 Remote Similarity NPC301449
0.6417 Remote Similarity NPC601290
0.641 Remote Similarity NPC159309
0.641 Remote Similarity NPC46665
0.641 Remote Similarity NPC86222
0.6404 Remote Similarity NPC473373
0.6396 Remote Similarity NPC214484
0.637 Remote Similarity NPC469775
0.6358 Remote Similarity NPC469777
0.6351 Remote Similarity NPC469774
0.6348 Remote Similarity NPC39211
0.6308 Remote Similarity NPC161717
0.6234 Remote Similarity NPC469772
0.6225 Remote Similarity NPC100925
0.622 Remote Similarity NPC191827
0.6198 Remote Similarity NPC281148
0.6154 Remote Similarity NPC469773
0.6134 Remote Similarity NPC10607
0.6127 Remote Similarity NPC472268
0.6121 Remote Similarity NPC150400
0.6106 Remote Similarity NPC204458
0.6098 Remote Similarity NPC80986
0.609 Remote Similarity NPC309223
0.609 Remote Similarity NPC302543
0.6083 Remote Similarity NPC475591
0.6083 Remote Similarity NPC236870
0.6061 Remote Similarity NPC471385
0.6056 Remote Similarity NPC297950
0.6053 Remote Similarity NPC1046
0.6053 Remote Similarity NPC78046
0.6048 Remote Similarity NPC473826
0.6047 Remote Similarity NPC54636
0.6033 Remote Similarity NPC222580
0.6033 Remote Similarity NPC609763
0.6031 Remote Similarity NPC13998
0.6031 Remote Similarity NPC286457
0.6017 Remote Similarity NPC213674
0.6016 Remote Similarity NPC219180
0.6016 Remote Similarity NPC251263
0.6 Remote Similarity NPC40775
0.6 Remote Similarity NPC251768
0.6 Remote Similarity NPC85154
0.5984 Remote Similarity NPC123522
0.5983 Remote Similarity NPC173583
0.5932 Remote Similarity NPC157868
0.592 Remote Similarity NPC104137
0.592 Remote Similarity NPC26626
0.5912 Remote Similarity NPC102505
0.5912 Remote Similarity NPC488514
0.5899 Remote Similarity NPC33012
0.5891 Remote Similarity NPC166422
0.5882 Remote Similarity NPC263756
0.5873 Remote Similarity NPC11242
0.5868 Remote Similarity NPC101744
0.5865 Remote Similarity NPC470876
0.5847 Remote Similarity NPC58448
0.5841 Remote Similarity NPC256798
0.5833 Remote Similarity NPC192791
0.5828 Remote Similarity NPC472269
0.5827 Remote Similarity NPC8524
0.5775 Remote Similarity NPC475368
0.575 Remote Similarity NPC473343
0.575 Remote Similarity NPC76497
0.5738 Remote Similarity NPC480475
0.5692 Remote Similarity NPC471384
0.5691 Remote Similarity NPC470515
0.5676 Remote Similarity NPC237503
0.5672 Remote Similarity NPC480418
0.5649 Remote Similarity NPC480419
0.5639 Remote Similarity NPC4749
0.5636 Remote Similarity NPC167383
0.5625 Remote Similarity NPC489208
0.561 Remote Similarity NPC164389
0.561 Remote Similarity NPC488526
0.5608 Remote Similarity NPC45606
0.56 Remote Similarity NPC134835
0.5573 Remote Similarity NPC133818
0.5571 Remote Similarity NPC480417
0.5556 Remote Similarity NPC189884
0.5556 Remote Similarity NPC473452
0.5556 Remote Similarity NPC138334
0.553 Remote Similarity NPC475209
0.5528 Remote Similarity NPC109588
0.5528 Remote Similarity NPC160415
0.5528 Remote Similarity NPC309714
0.5528 Remote Similarity NPC30289
0.5504 Remote Similarity NPC75287
0.55 Remote Similarity NPC139894
0.5492 Remote Similarity NPC161674
0.5492 Remote Similarity NPC473734
0.5489 Remote Similarity NPC471550
0.5484 Remote Similarity NPC173859
0.5484 Remote Similarity NPC148603
0.5481 Remote Similarity NPC21691
0.5476 Remote Similarity NPC469821
0.5455 Remote Similarity NPC23020
0.5455 Remote Similarity NPC475899
0.5455 Remote Similarity NPC323341
0.5455 Remote Similarity NPC470911
0.544 Remote Similarity NPC258885
0.5433 Remote Similarity NPC73318
0.541 Remote Similarity NPC473884
0.541 Remote Similarity NPC470512
0.5403 Remote Similarity NPC117714
0.5391 Remote Similarity NPC324875
0.5391 Remote Similarity NPC292677
0.5385 Remote Similarity NPC209894
0.5373 Remote Similarity NPC283417
0.5373 Remote Similarity NPC200049
0.5349 Remote Similarity NPC480473
0.5349 Remote Similarity NPC480474
0.5339 Remote Similarity NPC161434
0.5328 Remote Similarity NPC480420
0.5323 Remote Similarity NPC242840
0.5317 Remote Similarity NPC68175
0.5315 Remote Similarity NPC489209
0.5303 Remote Similarity NPC610204

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC481080 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