Natural Product: NPC210569

Natural Product IDNPC210569
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
WWTDJMJOCXHBFC-QWVLWBDESA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL498920
PubChem CID 10102850
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 WWTDJMJOCXHBFC-QWVLWBDESA-N
Standard InCHI InChI=1S/C56H90O28/c1-20-7-10-56(74-18-20)21(2)34-29(84-56)12-25-23-6-5-22-11-28(26(61)13-55(22,4)24(23)8-9-54(25,34)3)75-50-43(71)40(68)45(33(17-60)79-50)80-53-48(47(38(66)32(16-59)78-53)82-49-41(69)35(63)27(62)19-73-49)83-52-44(72)46(37(65)31(15-58)77-52)81-51-42(70)39(67)36(64)30(14-57)76-51/h5,20-21,23-53,57-72H,6-19H2,1-4H3/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+,52+,53+,54+,55+,56-/m1/s1
SMILES C[C@@H]1CC[C@@]2([C@@H](C)[C@H]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[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:   1210.56 Volume:   1126.5
?
Van der Waals volume.
Dense:   1.075 LogP:   0.163
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   0.978
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.089
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   14.0 Rigid Bonds:   60.0
TPSA:   434.44
?
Topological Polar Surface Area.
H-Bond Acceptor:   28.0
H-Bond Donor:   16.0 Rings:   11.0
Heavy Atoms:   28.0

MedChem Properties

QED Drug-Likeness Score:   0.072 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   7.747 Fsp3:   0.964
MCE-18:   291.564
?
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:   0.544 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:   0.413 Promiscuous compounds:   0.009

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -7.207 MDCK Permeability:   -4.949
Pgp-inhibitor:   0.0 Pgp-substrate:   0.968
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):   0.786
20% Bioavailability (F20%):   0.119 30% Bioavailability (F30%):   1.0
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.001 MRP1:   0.001
Plasma Protein Binding (PPB):   39.563% Volume Distribution (VD):   -0.409
Fu: 41.148%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.012
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:   0.004
CYP3A4-inhibitor:   0.995 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.465
HLM stability:   0.348
?
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):  -0.776 Half-life (T1/2):  3.776

ADMET: Toxicity

hERG Blockers:  0.001 hERG Blockers (10um):  0.0
Human Hepatotoxicity (H-HT):  0.621 Drug-induced Liver Injury (DILI):  0.991
AMES Toxicity:  0.996 Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.0 Skin Sensitization:  1.0
Carcinogencity:  0.021 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.623 Drug-induced Nephrotoxicity:  0.987
Genotoxicity:  0.003 RPMI-8226 Immunitoxicity:  0.498
A549 Cytotoxicity:  0.994 Hek293 Cytotoxicity:  0.954
BCF:   0.901
?
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:   3.184
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.423
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   3.497
?
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 NPC210569 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
0.934 High Similarity NPC31896
0.9196 High Similarity NPC263359
0.886 High Similarity NPC244431
0.8596 High Similarity NPC79900
0.7899 Intermediate Similarity NPC32707
0.7895 Intermediate Similarity NPC256983
0.7863 Intermediate Similarity NPC248202
0.7623 Intermediate Similarity NPC305771
0.7623 Intermediate Similarity NPC94072
0.7623 Intermediate Similarity NPC169816
0.7603 Intermediate Similarity NPC208832
0.7586 Intermediate Similarity NPC132080
0.7377 Intermediate Similarity NPC15918
0.7368 Intermediate Similarity NPC115165
0.7328 Intermediate Similarity NPC232037
0.7311 Intermediate Similarity NPC167183
0.7288 Intermediate Similarity NPC477811
0.7281 Intermediate Similarity NPC308459
0.7241 Intermediate Similarity NPC473518
0.7203 Intermediate Similarity NPC476112
0.7203 Intermediate Similarity NPC307534
0.7049 Intermediate Similarity NPC190939
0.6992 Remote Similarity NPC480556
0.6983 Remote Similarity NPC97700
0.6983 Remote Similarity NPC184617
0.6983 Remote Similarity NPC30856
0.6967 Remote Similarity NPC470866
0.6917 Remote Similarity NPC470862
0.681 Remote Similarity NPC300557
0.675 Remote Similarity NPC232611
0.6746 Remote Similarity NPC220836
0.6696 Remote Similarity NPC473601
0.6667 Remote Similarity NPC330026
0.6638 Remote Similarity NPC602423
0.6585 Remote Similarity NPC480553
0.6581 Remote Similarity NPC477809
0.6557 Remote Similarity NPC470864
0.6535 Remote Similarity NPC477807
0.6529 Remote Similarity NPC475625
0.6508 Remote Similarity NPC94086
0.6508 Remote Similarity NPC473817
0.6504 Remote Similarity NPC83137
0.6484 Remote Similarity NPC477808
0.6475 Remote Similarity NPC197003
0.6466 Remote Similarity NPC475351
0.6429 Remote Similarity NPC470867
0.6423 Remote Similarity NPC480554
0.6406 Remote Similarity NPC473505
0.6393 Remote Similarity NPC32361
0.6393 Remote Similarity NPC116756
0.6393 Remote Similarity NPC309278
0.6379 Remote Similarity NPC14704
0.626 Remote Similarity NPC475333
0.626 Remote Similarity NPC224098
0.626 Remote Similarity NPC208383
0.6222 Remote Similarity NPC481190
0.6207 Remote Similarity NPC470432
0.6207 Remote Similarity NPC230507
0.619 Remote Similarity NPC233433
0.6116 Remote Similarity NPC6806
0.6066 Remote Similarity NPC151134
0.5982 Remote Similarity NPC181845
0.5969 Remote Similarity NPC232054
0.5935 Remote Similarity NPC480555
0.5935 Remote Similarity NPC150372
0.5915 Remote Similarity NPC481189
0.5909 Remote Similarity NPC224314
0.5862 Remote Similarity NPC206003
0.5862 Remote Similarity NPC473610
0.5854 Remote Similarity NPC51172
0.5854 Remote Similarity NPC49032
0.5845 Remote Similarity NPC329820
0.5814 Remote Similarity NPC84111
0.5814 Remote Similarity NPC287483
0.5814 Remote Similarity NPC470865
0.5776 Remote Similarity NPC250393
0.5764 Remote Similarity NPC329727
0.5748 Remote Similarity NPC470861
0.5714 Remote Similarity NPC475319
0.5704 Remote Similarity NPC329807
0.5702 Remote Similarity NPC113044
0.5702 Remote Similarity NPC283829
0.5702 Remote Similarity NPC161676
0.5691 Remote Similarity NPC470433
0.5691 Remote Similarity NPC46190
0.5691 Remote Similarity NPC171073
0.5669 Remote Similarity NPC269297
0.5669 Remote Similarity NPC222202
0.5669 Remote Similarity NPC475550
0.5659 Remote Similarity NPC218571
0.5659 Remote Similarity NPC487615
0.5659 Remote Similarity NPC92710
0.5603 Remote Similarity NPC234352
0.5591 Remote Similarity NPC51520
0.5591 Remote Similarity NPC303069
0.5581 Remote Similarity NPC194207
0.5581 Remote Similarity NPC22779
0.5517 Remote Similarity NPC325828
0.5512 Remote Similarity NPC294129
0.5455 Remote Similarity NPC107962
0.5426 Remote Similarity NPC470863
0.5354 Remote Similarity NPC249553
0.5333 Remote Similarity NPC121453
0.529 Remote Similarity NPC273002
0.5285 Remote Similarity NPC125324
0.5276 Remote Similarity NPC248746
0.5271 Remote Similarity NPC98018
0.5271 Remote Similarity NPC284104
0.5271 Remote Similarity NPC103616
0.5271 Remote Similarity NPC102016
0.5271 Remote Similarity NPC95051
0.5194 Remote Similarity NPC128572
0.5188 Remote Similarity NPC108072
0.512 Remote Similarity NPC195297
0.5109 Remote Similarity NPC262050
0.5083 Remote Similarity NPC294686
0.5078 Remote Similarity NPC485603
0.5041 Remote Similarity NPC107188
0.5038 Remote Similarity NPC13193

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC210569 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
0.5517 Remote Similarity NPD8171 Phase 2
0.504 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