Natural Product: NPC575105

Natural Product IDNPC575105
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
26-O-beta-D-glucopyranosyl]-22alpha-methoxy-(25R)-furostan-3beta,26-diol 3-O-{beta-D-glucopyranosyl-(1→2)-[beta-D-glucopyranoside}
IUPAC Name (3~{S},4~{R},5~{R},6~{S})-2-[(2~{R})-4-[(1~{R},2~{S},4~{S},6~{R},7~{S},8~{R},9~{S},12~{S},13~{S},16~{S})-16-[(3~{R},4~{S},5~{S},6~{R})-4,5-dihydroxy-6-(hydroxymethyl)-3-[(3~{R},4~{S},5~{S},6~{R})-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydropyran-2-yl]oxy-tetrahydropyran-2-yl]oxy-6-methoxy-7,9,13-trimethyl-5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosan-6-yl]-2-methyl-butoxy]-6-(hydroxymethyl)tetrahydropyran-3,4,5-triol
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID n.a.
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]

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 FDASUPFDHLZNSK-UHKUVBCASA-N
Standard InCHI InChI=1S/C46H78O19/c1-20(19-59-41-38(56)35(53)32(50)28(16-47)61-41)8-13-46(58-5)21(2)31-27(65-46)15-26-24-7-6-22-14-23(9-11-44(22,3)25(24)10-12-45(26,31)4)60-43-40(37(55)34(52)30(18-49)63-43)64-42-39(57)36(54)33(51)29(17-48)62-42/h20-43,47-57H,6-19H2,1-5H3/t20-,21+,22?,23+,24-,25+,26+,27+,28+,29-,30-,31+,32+,33-,34-,35-,36+,37+,38+,39-,40-,41?,42?,43?,44+,45+,46-/m1/s1
SMILES CO[C@]1(CC[C@@H](C)COC2O[C@@H](CO)[C@H](O)[C@@H](O)[C@@H]2O)O[C@H]2C[C@H]3[C@@H]4CCC5C[C@@H](OC6O[C@H](CO)[C@@H](O)[C@H](O)[C@H]6OC6O[C@H](CO)[C@@H](O)[C@H](O)[C@H]6O)CC[C@]5(C)[C@H]4CC[C@]3(C)[C@H]2[C@@H]1C

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   934.51 Volume:   902.734
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Van der Waals volume.
Dense:   1.035 LogP:   1.228
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.287
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -4.684
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The logarithm of aqueous solubility value.
Rotatable Bonds:   14.0 Rigid Bonds:   42.0
TPSA:   296.37
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Topological Polar Surface Area.
H-Bond Acceptor:   19.0
H-Bond Donor:   11.0 Rings:   8.0
Heavy Atoms:   19.0

MedChem Properties

QED Drug-Likeness Score:   0.092 GASA:   1.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   6.379 Fsp3:   1.0
MCE-18:   156.13
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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:   0.568 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.009
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.0
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.241 Promiscuous compounds:   0.003

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.66 MDCK Permeability:   -5.031
Pgp-inhibitor:   0.0 Pgp-substrate:   0.56
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):   0.078
20% Bioavailability (F20%):   0.102 30% Bioavailability (F30%):   0.999
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.002 MRP1:   0.001
Plasma Protein Binding (PPB):   58.94% Volume Distribution (VD):   -0.336
Fu: 29.069%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.057
BSEP inhibitor:   0.002

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:   0.999 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.992
HLM stability:   0.017
?
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):  0.004 Half-life (T1/2):  3.007

ADMET: Toxicity

hERG Blockers:  0.003 hERG Blockers (10um):  0.042
Human Hepatotoxicity (H-HT):  0.799 Drug-induced Liver Injury (DILI):  0.845
AMES Toxicity:  0.752 Rat Oral Acute Toxicity:  0.002
Maximum Recommended Daily Dose:  0.003 Skin Sensitization:  1.0
Carcinogencity:  0.439 Eye Corrosion:  0.0
Eye Irritation:  0.001 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.002 Ototoxicity:  0.998
Hematotoxicity:  0.072 Drug-induced Nephrotoxicity:  0.974
Genotoxicity:  0.011 RPMI-8226 Immunitoxicity:  0.126
A549 Cytotoxicity:  0.421 Hek293 Cytotoxicity:  0.492
BCF:   1.598
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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:   3.583
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.958
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.108
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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
NPO15006 Asparagus africanus Species Asparagaceae Eukaryota n.a. n.a. n.a. PMID[9358645]
NPO15006 Asparagus africanus Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO15006 Asparagus africanus Species Asparagaceae 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 NPC575105 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
0.8659 High Similarity NPC297348
0.8659 High Similarity NPC249204
0.8659 High Similarity NPC48339
0.8659 High Similarity NPC141769
0.8659 High Similarity NPC477547
0.8242 Intermediate Similarity NPC475643
0.8235 Intermediate Similarity NPC477451
0.8161 Intermediate Similarity NPC211354
0.7778 Intermediate Similarity NPC107962
0.734 Intermediate Similarity NPC160426
0.7303 Intermediate Similarity NPC291203
0.7303 Intermediate Similarity NPC217205
0.7157 Intermediate Similarity NPC470864
0.7129 Intermediate Similarity NPC116756
0.7128 Intermediate Similarity NPC6295
0.7111 Intermediate Similarity NPC294686
0.7065 Intermediate Similarity NPC206003
0.7065 Intermediate Similarity NPC473610
0.6923 Remote Similarity NPC234352
0.6907 Remote Similarity NPC475351
0.69 Remote Similarity NPC128572
0.6882 Remote Similarity NPC128123
0.6822 Remote Similarity NPC470866
0.6813 Remote Similarity NPC325828
0.6809 Remote Similarity NPC107188
0.6809 Remote Similarity NPC19400
0.6796 Remote Similarity NPC475625
0.6774 Remote Similarity NPC222731
0.6571 Remote Similarity NPC194207
0.6571 Remote Similarity NPC22779
0.6535 Remote Similarity NPC92890
0.6465 Remote Similarity NPC113044
0.6465 Remote Similarity NPC283829
0.6465 Remote Similarity NPC161676
0.6452 Remote Similarity NPC177834
0.6421 Remote Similarity NPC474399
0.6346 Remote Similarity NPC97700
0.6346 Remote Similarity NPC30856
0.6321 Remote Similarity NPC309278
0.6311 Remote Similarity NPC471464
0.6289 Remote Similarity NPC54619
0.6273 Remote Similarity NPC232054
0.6263 Remote Similarity NPC125324
0.625 Remote Similarity NPC250393
0.619 Remote Similarity NPC184617
0.6162 Remote Similarity NPC485601
0.6154 Remote Similarity NPC51172
0.6154 Remote Similarity NPC49032
0.6147 Remote Similarity NPC470862
0.6111 Remote Similarity NPC232611
0.6091 Remote Similarity NPC132080
0.6064 Remote Similarity NPC485594
0.6058 Remote Similarity NPC477809
0.604 Remote Similarity NPC141433
0.5941 Remote Similarity NPC485595
0.5882 Remote Similarity NPC195297
0.5833 Remote Similarity NPC475319
0.5818 Remote Similarity NPC232037
0.5714 Remote Similarity NPC473601
0.5684 Remote Similarity NPC24960
0.567 Remote Similarity NPC181845
0.5648 Remote Similarity NPC480555
0.5648 Remote Similarity NPC150372
0.5566 Remote Similarity NPC98696
0.5514 Remote Similarity NPC485603
0.55 Remote Similarity NPC210157
0.5472 Remote Similarity NPC485605
0.5439 Remote Similarity NPC83137
0.5437 Remote Similarity NPC264101
0.5413 Remote Similarity NPC300557
0.5405 Remote Similarity NPC115165
0.5391 Remote Similarity NPC233433
0.5391 Remote Similarity NPC480553
0.5385 Remote Similarity NPC215408
0.5377 Remote Similarity NPC305423
0.537 Remote Similarity NPC470433
0.537 Remote Similarity NPC46190
0.537 Remote Similarity NPC171073
0.5368 Remote Similarity NPC277715
0.5364 Remote Similarity NPC485604
0.5361 Remote Similarity NPC485600
0.5357 Remote Similarity NPC470863
0.534 Remote Similarity NPC306131
0.534 Remote Similarity NPC200802
0.5315 Remote Similarity NPC98018
0.5315 Remote Similarity NPC284104
0.5315 Remote Similarity NPC103616
0.531 Remote Similarity NPC475333
0.531 Remote Similarity NPC224098
0.531 Remote Similarity NPC208383
0.5294 Remote Similarity NPC292467
0.5229 Remote Similarity NPC602423
0.5217 Remote Similarity NPC108072
0.5217 Remote Similarity NPC480554
0.5207 Remote Similarity NPC220836
0.5167 Remote Similarity NPC480556
0.5161 Remote Similarity NPC263359
0.5149 Remote Similarity NPC485602
0.5128 Remote Similarity NPC84111
0.5128 Remote Similarity NPC287483
0.5128 Remote Similarity NPC470865
0.5126 Remote Similarity NPC470867
0.5102 Remote Similarity NPC473774
0.5102 Remote Similarity NPC481419
0.5102 Remote Similarity NPC481417
0.5093 Remote Similarity NPC14704
0.5089 Remote Similarity NPC151134
0.5088 Remote Similarity NPC269297
0.5088 Remote Similarity NPC222202
0.5043 Remote Similarity NPC476112
0.5043 Remote Similarity NPC13193
0.5043 Remote Similarity NPC307534

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC575105 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
0.6813 Remote Similarity NPD8171 Phase 2
0.5784 Remote Similarity NPD8170 Phase 2

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