Natural Product: NPC126918

Natural Product IDNPC126918
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
AAJHVVLGKCKBSH-HSZGLWAXSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 11968931
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0001013] Steroidal glycosides
          • [CHEMONTID:0002364] Steroidal 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 AAJHVVLGKCKBSH-HSZGLWAXSA-N
Standard InCHI InChI=1S/C51H82O23/c1-20-31-27(73-51(20)13-12-48(3,74-51)19-65-44-38(61)36(59)33(56)28(16-52)68-44)15-26-24-7-6-22-14-23(8-10-49(22,4)25(24)9-11-50(26,31)5)67-47-43(72-46-40(63)37(60)34(57)29(17-53)69-46)41(64)42(30(18-54)70-47)71-45-39(62)35(58)32(55)21(2)66-45/h6,20-21,23-47,52-64H,7-19H2,1-5H3/t20-,21-,23?,24+,25-,26-,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-/m0/s1
SMILES C[C@H]1[C@H]2[C@H](C[C@H]3[C@@H]4CC=C5CC(CC[C@]5(C)[C@H]4CC[C@]23C)O[C@H]2[C@@H]([C@H]([C@@H]([C@@H](CO)O2)O[C@H]2[C@@H]([C@@H]([C@@H]([C@H](C)O2)O)O)O)O)O[C@H]2[C@@H]([C@H]([C@@H]([C@@H](CO)O2)O)O)O)O[C@@]21CC[C@@](C)(CO[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O2

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1062.52 Volume:   1004.626
?
Van der Waals volume.
Dense:   1.058 LogP:   0.33
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.258
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.123
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The logarithm of aqueous solubility value.
Rotatable Bonds:   12.0 Rigid Bonds:   53.0
TPSA:   355.29
?
Topological Polar Surface Area.
H-Bond Acceptor:   23.0
H-Bond Donor:   13.0 Rings:   10.0
Heavy Atoms:   23.0

MedChem Properties

QED Drug-Likeness Score:   0.088 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.296 Fsp3:   0.961
MCE-18:   266.0
?
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:   0.547 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.004
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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:   0.236 Promiscuous compounds:   0.018

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.923 MDCK Permeability:   -4.887
Pgp-inhibitor:   0.0 Pgp-substrate:   0.792
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):   0.983
20% Bioavailability (F20%):   0.828 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.01 MRP1:   0.096
Plasma Protein Binding (PPB):   61.967% Volume Distribution (VD):   -0.381
Fu: 29.635%
?
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:   0.004 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.001
HLM stability:   0.016
?
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):  -0.349 Half-life (T1/2):  3.329

ADMET: Toxicity

hERG Blockers:  0.001 hERG Blockers (10um):  0.002
Human Hepatotoxicity (H-HT):  0.738 Drug-induced Liver Injury (DILI):  0.984
AMES Toxicity:  0.997 Rat Oral Acute Toxicity:  0.001
Maximum Recommended Daily Dose:  0.0 Skin Sensitization:  1.0
Carcinogencity:  0.127 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.866 Drug-induced Nephrotoxicity:  0.994
Genotoxicity:  0.372 RPMI-8226 Immunitoxicity:  0.374
A549 Cytotoxicity:  0.996 Hek293 Cytotoxicity:  0.888
BCF:   1.378
?
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:   3.351
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.479
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   3.746
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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
NPO16509 Avena sativa Species Poaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jarmap.2018.11.004]
NPO16509 Avena sativa Species Poaceae Eukaryota n.a. n.a. n.a. PMID[6705789]
NPO16509 Avena sativa Species Poaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16509 Avena sativa Species Poaceae Eukaryota n.a. n.a. Database[FooDB]
NPO16509 Avena sativa Species Poaceae Eukaryota Hay n.a. n.a. Database[FooDB]
NPO16509 Avena sativa Species Poaceae Eukaryota Hull Husk n.a. n.a. Database[FooDB]
NPO16509 Avena sativa Species Poaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO16509 Avena sativa Species Poaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO16509 Avena sativa Species Poaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO16509 Avena sativa Species Poaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO16509 Avena sativa Species Poaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO16509 Avena sativa Species Poaceae Eukaryota n.a. n.a. Database[FooDB]
NPO16509 Avena sativa Species Poaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16509 Avena sativa Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16509 Avena sativa Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16509 Avena sativa Species Poaceae 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 NPC126918 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
0.7981 Intermediate Similarity NPC480555
0.7981 Intermediate Similarity NPC150372
0.7944 Intermediate Similarity NPC194207
0.7944 Intermediate Similarity NPC22779
0.7692 Intermediate Similarity NPC470433
0.7692 Intermediate Similarity NPC46190
0.7692 Intermediate Similarity NPC171073
0.7619 Intermediate Similarity NPC248746
0.7589 Intermediate Similarity NPC232054
0.7547 Intermediate Similarity NPC42171
0.7523 Intermediate Similarity NPC475333
0.7523 Intermediate Similarity NPC224098
0.7523 Intermediate Similarity NPC208383
0.7411 Intermediate Similarity NPC480553
0.7273 Intermediate Similarity NPC269297
0.7273 Intermediate Similarity NPC222202
0.7232 Intermediate Similarity NPC480554
0.7094 Intermediate Similarity NPC480556
0.7048 Intermediate Similarity NPC94272
0.6916 Remote Similarity NPC113044
0.6916 Remote Similarity NPC283829
0.6916 Remote Similarity NPC161676
0.6909 Remote Similarity NPC6806
0.6786 Remote Similarity NPC73243
0.6786 Remote Similarity NPC244086
0.6786 Remote Similarity NPC84956
0.675 Remote Similarity NPC224314
0.6696 Remote Similarity NPC475182
0.6667 Remote Similarity NPC247037
0.6609 Remote Similarity NPC309278
0.6607 Remote Similarity NPC300557
0.6518 Remote Similarity NPC477809
0.6496 Remote Similarity NPC249265
0.6466 Remote Similarity NPC13193
0.6441 Remote Similarity NPC23808
0.6441 Remote Similarity NPC87998
0.6429 Remote Similarity NPC602423
0.6422 Remote Similarity NPC470432
0.6422 Remote Similarity NPC230507
0.6325 Remote Similarity NPC32361
0.6306 Remote Similarity NPC305423
0.629 Remote Similarity NPC477808
0.6273 Remote Similarity NPC6295
0.6228 Remote Similarity NPC122819
0.6198 Remote Similarity NPC308140
0.619 Remote Similarity NPC181845
0.6102 Remote Similarity NPC475550
0.6018 Remote Similarity NPC14704
0.6 Remote Similarity NPC19400
0.5982 Remote Similarity NPC485595
0.5943 Remote Similarity NPC165439
0.5935 Remote Similarity NPC287885
0.5913 Remote Similarity NPC98696
0.5897 Remote Similarity NPC124677
0.5833 Remote Similarity NPC486386
0.5738 Remote Similarity NPC254255
0.5726 Remote Similarity NPC265275
0.5726 Remote Similarity NPC477811
0.5667 Remote Similarity NPC102016
0.5667 Remote Similarity NPC95051
0.5652 Remote Similarity NPC141433
0.5652 Remote Similarity NPC195297
0.55 Remote Similarity NPC249553
0.547 Remote Similarity NPC160426
0.544 Remote Similarity NPC218571
0.544 Remote Similarity NPC487615
0.5372 Remote Similarity NPC471464
0.5333 Remote Similarity NPC475643
0.5328 Remote Similarity NPC150057
0.5328 Remote Similarity NPC147753
0.5312 Remote Similarity NPC31896
0.531 Remote Similarity NPC477451
0.525 Remote Similarity NPC40440
0.525 Remote Similarity NPC486388
0.5246 Remote Similarity NPC182900
0.521 Remote Similarity NPC470748
0.5203 Remote Similarity NPC128572
0.5172 Remote Similarity NPC306131
0.5172 Remote Similarity NPC211354
0.5172 Remote Similarity NPC200802
0.5169 Remote Similarity NPC15249
0.5169 Remote Similarity NPC306991
0.5169 Remote Similarity NPC25455
0.5133 Remote Similarity NPC297348
0.5133 Remote Similarity NPC249204
0.5133 Remote Similarity NPC48339
0.5133 Remote Similarity NPC141769
0.5133 Remote Similarity NPC477547
0.5085 Remote Similarity NPC107962
0.5085 Remote Similarity NPC295980
0.5083 Remote Similarity NPC600116
0.5037 Remote Similarity NPC210569

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC126918 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
0.6228 Remote Similarity NPD8449 Approved
0.5328 Remote Similarity NPD8450 Suspended

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