Natural Product: NPC256983

Natural Product IDNPC256983
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
VJVXEDWJFVNCJF-FEIWAIHWSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL500203
PubChem CID 11967644
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0001013] Steroidal glycosides

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 VJVXEDWJFVNCJF-FEIWAIHWSA-N
Standard InCHI InChI=1S/C51H80O28/c1-16-29-24(70-44(16)68)9-20-18-5-4-17-8-23(21(56)10-51(17,3)19(18)6-7-50(20,29)2)71-46-38(66)35(63)40(28(14-55)75-46)76-49-43(42(33(61)27(13-54)74-49)78-45-36(64)30(58)22(57)15-69-45)79-48-39(67)41(32(60)26(12-53)73-48)77-47-37(65)34(62)31(59)25(11-52)72-47/h4,16,18-43,45-49,52-67H,5-15H2,1-3H3/t16-,18+,19-,20-,21+,22+,23+,24-,25+,26+,27+,28+,29-,30-,31+,32+,33+,34-,35+,36+,37+,38+,39+,40-,41-,42-,43+,45-,46+,47-,48-,49-,50-,51-/m0/s1
SMILES OC[C@H]1O[C@@H](O[C@@H]2CC3=CC[C@@H]4[C@@H]([C@]3(C[C@H]2O)C)CC[C@]2([C@H]4C[C@H]3[C@@H]2[C@@H](C(=O)O3)C)C)[C@@H]([C@H]([C@H]1O[C@@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O[C@@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)O[C@@H]1O[C@H](CO)[C@H]([C@@H]([C@H]1O)O)O)O)O[C@@H]1OC[C@H]([C@@H]([C@H]1O)O)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1140.48 Volume:   1045.941
?
Van der Waals volume.
Dense:   1.09 LogP:   -0.729
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.2
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -2.663
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   14.0 Rigid Bonds:   55.0
TPSA:   442.28
?
Topological Polar Surface Area.
H-Bond Acceptor:   28.0
H-Bond Donor:   16.0 Rings:   10.0
Heavy Atoms:   28.0

MedChem Properties

QED Drug-Likeness Score:   0.057 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.093 Fsp3:   0.941
MCE-18:   197.98
?
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:   0.537 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:   0.439 Promiscuous compounds:   0.025

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -7.34 MDCK Permeability:   -5.094
Pgp-inhibitor:   0.0 Pgp-substrate:   0.935
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):   0.992
20% Bioavailability (F20%):   0.179 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.001 MRP1:   0.003
Plasma Protein Binding (PPB):   39.938% Volume Distribution (VD):   -0.43
Fu: 41.937%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 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:   0.666 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.019
HLM stability:   0.012
?
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):  -0.687 Half-life (T1/2):  3.8

ADMET: Toxicity

hERG Blockers:  0.0 hERG Blockers (10um):  0.0
Human Hepatotoxicity (H-HT):  0.624 Drug-induced Liver Injury (DILI):  0.979
AMES Toxicity:  0.993 Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.0 Skin Sensitization:  1.0
Carcinogencity:  0.024 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.928 Drug-induced Nephrotoxicity:  0.992
Genotoxicity:  0.022 RPMI-8226 Immunitoxicity:  0.269
A549 Cytotoxicity:  0.988 Hek293 Cytotoxicity:  0.734
BCF:   0.407
?
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:   3.043
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.437
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   3.49
?
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 NPC256983 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
0.8273 Intermediate Similarity NPC248202
0.8 Intermediate Similarity NPC308459
0.7895 Intermediate Similarity NPC210569
0.7692 Intermediate Similarity NPC244431
0.7692 Intermediate Similarity NPC263359
0.7672 Intermediate Similarity NPC208832
0.7281 Intermediate Similarity NPC31896
0.7241 Intermediate Similarity NPC190939
0.7143 Intermediate Similarity NPC79900
0.6942 Remote Similarity NPC32707
0.6638 Remote Similarity NPC197003
0.6364 Remote Similarity NPC167183
0.6172 Remote Similarity NPC305771
0.6172 Remote Similarity NPC94072
0.6172 Remote Similarity NPC169816
0.5938 Remote Similarity NPC15918
0.5806 Remote Similarity NPC84111
0.5806 Remote Similarity NPC287483
0.5806 Remote Similarity NPC132080
0.5806 Remote Similarity NPC470865
0.5738 Remote Similarity NPC470861
0.5669 Remote Similarity NPC470866
0.5645 Remote Similarity NPC218571
0.5645 Remote Similarity NPC487615
0.5645 Remote Similarity NPC92710
0.56 Remote Similarity NPC470862
0.5574 Remote Similarity NPC51520
0.5574 Remote Similarity NPC115165
0.5574 Remote Similarity NPC303069
0.5565 Remote Similarity NPC232037
0.5556 Remote Similarity NPC477811
0.5547 Remote Similarity NPC470867
0.5484 Remote Similarity NPC473518
0.5476 Remote Similarity NPC476112
0.5476 Remote Similarity NPC307534
0.544 Remote Similarity NPC232611
0.5403 Remote Similarity NPC470863
0.5379 Remote Similarity NPC220836
0.5379 Remote Similarity NPC273002
0.5344 Remote Similarity NPC480556
0.5308 Remote Similarity NPC262050
0.5276 Remote Similarity NPC470864
0.5242 Remote Similarity NPC97700
0.5242 Remote Similarity NPC98018
0.5242 Remote Similarity NPC184617
0.5242 Remote Similarity NPC30856
0.5242 Remote Similarity NPC284104
0.5242 Remote Similarity NPC103616
0.5242 Remote Similarity NPC102016
0.5242 Remote Similarity NPC95051
0.5188 Remote Similarity NPC477807
0.5161 Remote Similarity NPC150057
0.5161 Remote Similarity NPC147753
0.5152 Remote Similarity NPC94086
0.5152 Remote Similarity NPC473817
0.5149 Remote Similarity NPC477808
0.5143 Remote Similarity NPC330026
0.5118 Remote Similarity NPC116756
0.5118 Remote Similarity NPC309278
0.5081 Remote Similarity NPC300557
0.5075 Remote Similarity NPC473505

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC256983 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
0.5161 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