Natural Product: NPC69831

Natural Product IDNPC69831
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
CEJNPQORURWPJT-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 164214
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 CEJNPQORURWPJT-UHFFFAOYSA-N
Standard InCHI InChI=1S/C53H90O22/c1-24(2)18-36(56)72-35-22-34-49(7)14-13-30(19-29(49)12-15-52(34,62)53(63)17-16-51(61,28(6)55)50(35,53)8)70-37-20-31(64-9)43(25(3)67-37)73-38-21-32(65-10)44(26(4)68-38)74-48-42(60)46(66-11)45(27(5)69-48)75-47-41(59)40(58)39(57)33(23-54)71-47/h24-35,37-48,54-55,57-63H,12-23H2,1-11H3
SMILES CC(C)CC(=O)OC1CC2C3(C)CCC(CC3CCC2(C2(CCC(C(C)O)(C12C)O)O)O)OC1CC(C(C(C)O1)OC1CC(C(C(C)O1)OC1C(C(C(C(C)O1)OC1C(C(C(C(CO)O1)O)O)O)OC)O)OC)OC

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1078.59 Volume:   1047.541
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Van der Waals volume.
Dense:   1.03 LogP:   1.975
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.37
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -2.645
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The logarithm of aqueous solubility value.
Rotatable Bonds:   17.0 Rigid Bonds:   45.0
TPSA:   309.9
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Topological Polar Surface Area.
H-Bond Acceptor:   22.0
H-Bond Donor:   9.0 Rings:   8.0
Heavy Atoms:   22.0

MedChem Properties

QED Drug-Likeness Score:   0.076 GASA:   1.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   6.938 Fsp3:   0.981
MCE-18:   173.105
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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:   0.0 Fluc inhibitor:   0.0
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.002
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.189
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.452 Promiscuous compounds:   0.003

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.747 MDCK Permeability:   -5.13
Pgp-inhibitor:   0.0 Pgp-substrate:   1.0
PAMPA:   1.0
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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):   0.999
20% Bioavailability (F20%):   0.311 30% Bioavailability (F30%):   0.929
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.012 MRP1:   1.0
Plasma Protein Binding (PPB):   20.473% Volume Distribution (VD):   -0.515
Fu: 75.54%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   0.0
OATP1B3 inhibitor:   0.049 BCRP inhibitor:   0.0
BSEP inhibitor:   0.026

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   1.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.502 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.995 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.084 CYP2C8-inhibitor:   0.0
HLM stability:   0.0
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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):  0.495 Half-life (T1/2):  6.0

ADMET: Toxicity

hERG Blockers:  0.152 hERG Blockers (10um):  0.359
Human Hepatotoxicity (H-HT):  0.551 Drug-induced Liver Injury (DILI):  0.134
AMES Toxicity:  0.787 Rat Oral Acute Toxicity:  0.399
Maximum Recommended Daily Dose:  0.484 Skin Sensitization:  0.154
Carcinogencity:  0.062 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.004
Drug-induced Neurotoxicity:  0.153 Ototoxicity:  1.0
Hematotoxicity:  0.014 Drug-induced Nephrotoxicity:  0.045
Genotoxicity:  0.1 RPMI-8226 Immunitoxicity:  0.314
A549 Cytotoxicity:  0.045 Hek293 Cytotoxicity:  0.781
BCF:   0.563
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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:   3.716
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.795
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.226
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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
NPO3545 Dracaena draco Species Asparagaceae Eukaryota bark n.a. n.a. PMID[12828464]
NPO3545 Dracaena draco Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3545 Dracaena draco Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3545 Dracaena draco Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3545 Dracaena draco Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3545 Dracaena draco 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 NPC69831 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
0.697 Remote Similarity NPC475358
0.697 Remote Similarity NPC473566
0.6154 Remote Similarity NPC102015
0.6053 Remote Similarity NPC70236
0.5702 Remote Similarity NPC475447
0.5487 Remote Similarity NPC474423
0.5378 Remote Similarity NPC473641
0.5378 Remote Similarity NPC475300
0.537 Remote Similarity NPC477492
0.5333 Remote Similarity NPC479353
0.5333 Remote Similarity NPC479354
0.5294 Remote Similarity NPC475218
0.5289 Remote Similarity NPC476092
0.5273 Remote Similarity NPC481661
0.5273 Remote Similarity NPC481655
0.5217 Remote Similarity NPC477493
0.5133 Remote Similarity NPC120390
0.5133 Remote Similarity NPC475419
0.5093 Remote Similarity NPC486143
0.5093 Remote Similarity NPC486142
0.5093 Remote Similarity NPC486149
0.5079 Remote Similarity NPC473797
0.5045 Remote Similarity NPC479357

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC69831 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