Natural Product: NPC167183

Natural Product IDNPC167183
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
JLNDSXHXXHCLHZ-YRBXTQJASA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL500012
PubChem CID 10677623
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 JLNDSXHXXHCLHZ-YRBXTQJASA-N
Standard InCHI InChI=1S/C50H80O24/c1-19-7-10-49(66-17-19)20(2)50(64)31(74-49)12-24-22-6-5-21-11-27(25(54)13-47(21,3)23(22)8-9-48(24,50)4)67-44-39(63)36(60)40(30(16-53)70-44)71-46-42(73-45-38(62)35(59)33(57)28(14-51)68-45)41(34(58)29(15-52)69-46)72-43-37(61)32(56)26(55)18-65-43/h5,19-20,22-46,51-64H,6-18H2,1-4H3/t19-,20-,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+,47+,48+,49-,50-/m1/s1
SMILES C[C@@H]1CC[C@@]2([C@@H](C)[C@]3([C@H](C[C@H]4[C@@H]5CC=C6C[C@H]([C@@H](C[C@]6(C)[C@H]5CC[C@]34C)O)O[C@H]3[C@@H]([C@H]([C@H]([C@@H](CO)O3)O[C@H]3[C@@H]([C@H]([C@@H]([C@@H](CO)O3)O)O[C@H]3[C@@H]([C@H]([C@@H](CO3)O)O)O)O[C@H]3[C@@H]([C@H]([C@@H]([C@@H](CO)O3)O)O)O)O)O)O2)O)OC1

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1064.5 Volume:   996.12
?
Van der Waals volume.
Dense:   1.069 LogP:   0.317
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.06
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -2.665
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   11.0 Rigid Bonds:   54.0
TPSA:   375.52
?
Topological Polar Surface Area.
H-Bond Acceptor:   24.0
H-Bond Donor:   14.0 Rings:   10.0
Heavy Atoms:   24.0

MedChem Properties

QED Drug-Likeness Score:   0.087 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.377 Fsp3:   0.96
MCE-18:   268.571
?
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:   0.618 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.002
?
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:   0.331 Promiscuous compounds:   0.045

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -7.068 MDCK Permeability:   -4.942
Pgp-inhibitor:   0.0 Pgp-substrate:   0.952
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):   0.709
20% Bioavailability (F20%):   0.316 30% Bioavailability (F30%):   0.998
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.009 MRP1:   0.004
Plasma Protein Binding (PPB):   44.601% Volume Distribution (VD):   -0.404
Fu: 37.441%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.048
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:   0.81 CYP3A4-substrate:   0.794
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.001
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):  -0.263 Half-life (T1/2):  3.506

ADMET: Toxicity

hERG Blockers:  0.003 hERG Blockers (10um):  0.003
Human Hepatotoxicity (H-HT):  0.621 Drug-induced Liver Injury (DILI):  0.962
AMES Toxicity:  0.99 Rat Oral Acute Toxicity:  0.001
Maximum Recommended Daily Dose:  0.002 Skin Sensitization:  1.0
Carcinogencity:  0.045 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.592 Drug-induced Nephrotoxicity:  0.983
Genotoxicity:  0.054 RPMI-8226 Immunitoxicity:  0.571
A549 Cytotoxicity:  0.989 Hek293 Cytotoxicity:  0.898
BCF:   0.797
?
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:   3.139
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.366
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   3.498
?
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
NPO27323 Cestrum nocturnum Species Solanaceae Eukaryota leaves n.a. n.a. PMID[11170659]
NPO27323 Cestrum nocturnum Species Solanaceae Eukaryota leaves n.a. n.a. PMID[12502329]
NPO27323 Cestrum nocturnum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO27323 Cestrum nocturnum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27323 Cestrum nocturnum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO27323 Cestrum nocturnum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO27323 Cestrum nocturnum Species Solanaceae 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 NPC167183 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
0.9346 High Similarity NPC32707
0.7768 Intermediate Similarity NPC31896
0.7311 Intermediate Similarity NPC210569
0.7025 Intermediate Similarity NPC79900
0.6957 Remote Similarity NPC197003
0.6855 Remote Similarity NPC263359
0.6754 Remote Similarity NPC308459
0.6587 Remote Similarity NPC244431
0.6557 Remote Similarity NPC190939
0.6504 Remote Similarity NPC248202
0.6364 Remote Similarity NPC256983
0.6299 Remote Similarity NPC208832
0.6154 Remote Similarity NPC124677
0.6121 Remote Similarity NPC469347
0.6034 Remote Similarity NPC40440
0.6 Remote Similarity NPC115165
0.5954 Remote Similarity NPC305771
0.5954 Remote Similarity NPC94072
0.5954 Remote Similarity NPC169816
0.5902 Remote Similarity NPC473518
0.5897 Remote Similarity NPC42482
0.584 Remote Similarity NPC477811
0.5725 Remote Similarity NPC15918
0.5656 Remote Similarity NPC97700
0.5656 Remote Similarity NPC30856
0.562 Remote Similarity NPC274200
0.56 Remote Similarity NPC232611
0.5492 Remote Similarity NPC300557
0.5372 Remote Similarity NPC473601
0.5349 Remote Similarity NPC233433
0.5349 Remote Similarity NPC132080
0.5328 Remote Similarity NPC602423
0.5285 Remote Similarity NPC469348
0.5276 Remote Similarity NPC116756
0.5276 Remote Similarity NPC309278
0.5224 Remote Similarity NPC477807
0.5194 Remote Similarity NPC218571
0.5194 Remote Similarity NPC487615
0.5185 Remote Similarity NPC477808
0.5164 Remote Similarity NPC475351
0.5161 Remote Similarity NPC477809
0.5156 Remote Similarity NPC32361
0.5154 Remote Similarity NPC83137
0.5128 Remote Similarity NPC474399
0.5128 Remote Similarity NPC86020
0.5118 Remote Similarity NPC51520
0.5118 Remote Similarity NPC303069
0.5116 Remote Similarity NPC232037
0.5079 Remote Similarity NPC156789
0.5074 Remote Similarity NPC220836
0.5039 Remote Similarity NPC475333
0.5039 Remote Similarity NPC224098
0.5039 Remote Similarity NPC208383
0.5038 Remote Similarity NPC476112
0.5038 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 NPC167183 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