Natural Product: NPC244591

Natural Product IDNPC244591
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
RZWGPDBWOSUYCQ-SCDJFGJSSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 24893672
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 RZWGPDBWOSUYCQ-SCDJFGJSSA-N
Standard InCHI InChI=1S/C57H94O29/c1-20-7-10-57(75-19-20)21(2)34-28(86-57)12-25-23-6-5-22-11-27(26(63)13-56(22,4)24(23)8-9-55(25,34)3)76-53-45(74)47(37(66)31(16-60)79-53)83-52-44(73)41(70)46(33(18-62)81-52)82-54-49(85-51-43(72)40(69)36(65)30(15-59)78-51)48(38(67)32(17-61)80-54)84-50-42(71)39(68)35(64)29(14-58)77-50/h20-54,58-74H,5-19H2,1-4H3/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-,47+,48+,49-,50+,51+,52+,53-,54+,55+,56+,57?/m1/s1
SMILES C[C@@H]1CCC2(C(C)C3C(CC4C5CC[C@H]6CC([C@@H](C[C@]6(C)C5CC[C@]34C)O)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]([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]([C@@H](CO)O3)O)O)O)O[C@H]3[C@@H]([C@H]([C@@H]([C@@H](CO)O3)O)O)O)O)O)O)O2)OC1

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1242.59 Volume:   1155.223
?
Van der Waals volume.
Dense:   1.076 LogP:   -0.515
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.432
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.328
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   15.0 Rigid Bonds:   60.0
TPSA:   454.67
?
Topological Polar Surface Area.
H-Bond Acceptor:   29.0
H-Bond Donor:   17.0 Rings:   11.0
Heavy Atoms:   29.0

MedChem Properties

QED Drug-Likeness Score:   0.068 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.721 Fsp3:   1.0
MCE-18:   295.842
?
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:   0.41 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.003
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.002
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.401 Promiscuous compounds:   0.004

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -7.472 MDCK Permeability:   -4.859
Pgp-inhibitor:   0.0 Pgp-substrate:   0.957
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):   0.001
20% Bioavailability (F20%):   0.001 30% Bioavailability (F30%):   0.999
50% Bioavailability (F50%):   0.993

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.023 MRP1:   0.047
Plasma Protein Binding (PPB):   36.011% Volume Distribution (VD):   -0.459
Fu: 48.249%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.001
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:   0.002 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.0
HLM stability:   0.083
?
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):  -1.276 Half-life (T1/2):  5.457

ADMET: Toxicity

hERG Blockers:  0.001 hERG Blockers (10um):  0.001
Human Hepatotoxicity (H-HT):  0.908 Drug-induced Liver Injury (DILI):  0.984
AMES Toxicity:  0.997 Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.0 Skin Sensitization:  1.0
Carcinogencity:  0.08 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.311 Drug-induced Nephrotoxicity:  0.975
Genotoxicity:  0.001 RPMI-8226 Immunitoxicity:  0.353
A549 Cytotoxicity:  0.993 Hek293 Cytotoxicity:  0.816
BCF:   1.031
?
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:   3.306
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.546
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   3.465
?
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
NPO24552 Capsicum frutescens Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11049 Solanum capsicastrum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO24552 Capsicum frutescens Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11049 Solanum capsicastrum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24552 Capsicum frutescens Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11049 Solanum capsicastrum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24552 Capsicum frutescens Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11049 Solanum capsicastrum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11049 Solanum capsicastrum 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 NPC244591 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
0.89 High Similarity NPC470862
0.8586 High Similarity NPC115165
0.8485 Intermediate Similarity NPC184617
0.835 Intermediate Similarity NPC83137
0.8037 Intermediate Similarity NPC470867
0.7925 Intermediate Similarity NPC132080
0.781 Intermediate Similarity NPC232611
0.78 Intermediate Similarity NPC473601
0.7672 Intermediate Similarity NPC481190
0.7642 Intermediate Similarity NPC232037
0.757 Intermediate Similarity NPC470864
0.7547 Intermediate Similarity NPC473518
0.7458 Intermediate Similarity NPC330026
0.7383 Intermediate Similarity NPC470861
0.7368 Intermediate Similarity NPC210569
0.7264 Intermediate Similarity NPC97700
0.7264 Intermediate Similarity NPC30856
0.7232 Intermediate Similarity NPC470866
0.7172 Intermediate Similarity NPC206003
0.7172 Intermediate Similarity NPC473610
0.7091 Intermediate Similarity NPC92710
0.7041 Intermediate Similarity NPC294686
0.7027 Intermediate Similarity NPC476112
0.7027 Intermediate Similarity NPC307534
0.699 Remote Similarity NPC195297
0.6869 Remote Similarity NPC234352
0.6852 Remote Similarity NPC151134
0.6838 Remote Similarity NPC220836
0.6768 Remote Similarity NPC325828
0.6757 Remote Similarity NPC475625
0.6754 Remote Similarity NPC31896
0.675 Remote Similarity NPC263359
0.6733 Remote Similarity NPC222731
0.6698 Remote Similarity NPC475351
0.6635 Remote Similarity NPC107962
0.6607 Remote Similarity NPC116756
0.6581 Remote Similarity NPC94086
0.6581 Remote Similarity NPC473817
0.6505 Remote Similarity NPC121453
0.6484 Remote Similarity NPC329820
0.6475 Remote Similarity NPC244431
0.6429 Remote Similarity NPC51520
0.6429 Remote Similarity NPC303069
0.6379 Remote Similarity NPC477811
0.6364 Remote Similarity NPC79900
0.6262 Remote Similarity NPC125324
0.6239 Remote Similarity NPC233433
0.6228 Remote Similarity NPC470863
0.6132 Remote Similarity NPC54619
0.6061 Remote Similarity NPC481189
0.6018 Remote Similarity NPC300557
0.5966 Remote Similarity NPC84111
0.5966 Remote Similarity NPC287483
0.5966 Remote Similarity NPC470865
0.5963 Remote Similarity NPC6295
0.5962 Remote Similarity NPC297348
0.5962 Remote Similarity NPC249204
0.5962 Remote Similarity NPC48339
0.5962 Remote Similarity NPC141769
0.5962 Remote Similarity NPC477547
0.5952 Remote Similarity NPC305771
0.5952 Remote Similarity NPC94072
0.5952 Remote Similarity NPC169816
0.5943 Remote Similarity NPC250393
0.5935 Remote Similarity NPC473505
0.5935 Remote Similarity NPC477807
0.5896 Remote Similarity NPC329727
0.5877 Remote Similarity NPC51172
0.5877 Remote Similarity NPC49032
0.5841 Remote Similarity NPC602423
0.5833 Remote Similarity NPC107188
0.5833 Remote Similarity NPC329807
0.5833 Remote Similarity NPC480553
0.5726 Remote Similarity NPC475319
0.5714 Remote Similarity NPC15918
0.5701 Remote Similarity NPC477451
0.5688 Remote Similarity NPC19400
0.5669 Remote Similarity NPC32707
0.5667 Remote Similarity NPC480554
0.5652 Remote Similarity NPC92890
0.5652 Remote Similarity NPC477809
0.56 Remote Similarity NPC248202
0.5575 Remote Similarity NPC14704
0.5575 Remote Similarity NPC160426
0.5574 Remote Similarity NPC256983
0.5545 Remote Similarity NPC211354
0.5512 Remote Similarity NPC477808
0.5429 Remote Similarity NPC24960
0.5426 Remote Similarity NPC208832
0.5398 Remote Similarity NPC470432
0.5398 Remote Similarity NPC230507
0.5378 Remote Similarity NPC98018
0.5378 Remote Similarity NPC284104
0.5378 Remote Similarity NPC103616
0.5372 Remote Similarity NPC309278
0.5354 Remote Similarity NPC480556
0.5294 Remote Similarity NPC128572
0.5271 Remote Similarity NPC273002
0.5263 Remote Similarity NPC485595
0.5246 Remote Similarity NPC32361
0.5197 Remote Similarity NPC262050
0.5185 Remote Similarity NPC485594
0.5182 Remote Similarity NPC131693
0.5182 Remote Similarity NPC475436
0.5167 Remote Similarity NPC480555
0.5167 Remote Similarity NPC150372
0.5143 Remote Similarity NPC277715
0.5118 Remote Similarity NPC167183
0.5083 Remote Similarity NPC6806
0.5042 Remote Similarity NPC475643
0.504 Remote Similarity NPC108072
0.5039 Remote Similarity NPC190939

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC244591 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
0.6768 Remote Similarity NPD8171 Phase 2
0.5963 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