Natural Product: NPC47529

Natural Product IDNPC47529
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
ANRCURCEMLFKEB-IYGDEICBSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID n.a.
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 ANRCURCEMLFKEB-IYGDEICBSA-N
Standard InCHI InChI=1S/C51H84O22/c1-21(19-65-45-41(62)39(60)36(57)31(17-52)69-45)9-14-51(64-6)22(2)33-30(73-51)16-28-26-8-7-24-15-25(10-12-49(24,4)27(26)11-13-50(28,33)5)68-48-44(72-47-42(63)38(59)34(55)23(3)67-47)43(37(58)32(18-53)70-48)71-46-40(61)35(56)29(54)20-66-46/h7,21-23,25-48,52-63H,8-20H2,1-6H3/t21-,22+,23+,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+/m1/s1
SMILES C[C@H](CC[C@]1([C@@H](C)[C@H]2[C@H](C[C@H]3[C@@H]4CC=C5C[C@H](CC[C@]5(C)[C@H]4CC[C@]23C)O[C@H]2[C@@H]([C@H]([C@@H]([C@@H](CO)O2)O)O[C@H]2[C@@H]([C@H]([C@@H](CO2)O)O)O)O[C@H]2[C@@H]([C@@H]([C@H]([C@H](C)O2)O)O)O)O1)OC)CO[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1048.55 Volume:   1004.392
?
Van der Waals volume.
Dense:   1.044 LogP:   1.259
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   2.189
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -4.269
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   15.0 Rigid Bonds:   48.0
TPSA:   335.06
?
Topological Polar Surface Area.
H-Bond Acceptor:   22.0
H-Bond Donor:   12.0 Rings:   9.0
Heavy Atoms:   22.0

MedChem Properties

QED Drug-Likeness Score:   0.081 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   6.812 Fsp3:   0.961
MCE-18:   175.36
?
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:   0.627 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:   0.0
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.295 Promiscuous compounds:   0.01

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.536 MDCK Permeability:   -5.077
Pgp-inhibitor:   0.0 Pgp-substrate:   0.941
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):   0.011
20% Bioavailability (F20%):   0.007 30% Bioavailability (F30%):   0.994
50% Bioavailability (F50%):   1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.001
Plasma Protein Binding (PPB):   46.165% Volume Distribution (VD):   -0.405
Fu: 39.25%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.114
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:   0.001
CYP3A4-inhibitor:   0.997 CYP3A4-substrate:   1.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.976
HLM stability:   0.043
?
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):  -0.137 Half-life (T1/2):  3.269

ADMET: Toxicity

hERG Blockers:  0.012 hERG Blockers (10um):  0.023
Human Hepatotoxicity (H-HT):  0.427 Drug-induced Liver Injury (DILI):  0.759
AMES Toxicity:  0.823 Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.001 Skin Sensitization:  1.0
Carcinogencity:  0.009 Eye Corrosion:  0.0
Eye Irritation:  0.0 Respiratory Toxicity:  0.0
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  1.0
Hematotoxicity:  0.194 Drug-induced Nephrotoxicity:  0.848
Genotoxicity:  0.0 RPMI-8226 Immunitoxicity:  0.242
A549 Cytotoxicity:  0.653 Hek293 Cytotoxicity:  0.562
BCF:   1.652
?
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:   3.438
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.702
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   3.991
?
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
NPO9062 Lilium longiflorum Thunb. Strain Liliaceae Eukaryota n.a. n.a. n.a. PMID[21524113]
NPO7703 Xanthorrhoea preissii Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9062 Lilium longiflorum Thunb. Strain Liliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO8173 Lupinus multiflorus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6023 Neurolaena venturana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9062 Lilium longiflorum Thunb. Strain Liliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9062 Lilium longiflorum Thunb. Strain Liliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6023 Neurolaena venturana Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7703 Xanthorrhoea preissii Species Asphodelaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2383 Mimosa acacioides Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5425 Polygala nyikensis Species Polygalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10340 Crepis rubra Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9062 Lilium longiflorum Thunb. Strain Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8173 Lupinus multiflorus Species Fabaceae 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 NPC47529 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
0.9495 High Similarity NPC309278
0.8431 Intermediate Similarity NPC300557
0.8426 Intermediate Similarity NPC232054
0.8235 Intermediate Similarity NPC602423
0.7963 Intermediate Similarity NPC194207
0.7963 Intermediate Similarity NPC22779
0.7727 Intermediate Similarity NPC218571
0.7727 Intermediate Similarity NPC487615
0.7479 Intermediate Similarity NPC263359
0.7387 Intermediate Similarity NPC475333
0.7387 Intermediate Similarity NPC224098
0.7387 Intermediate Similarity NPC208383
0.7273 Intermediate Similarity NPC102016
0.7273 Intermediate Similarity NPC95051
0.7232 Intermediate Similarity NPC116756
0.7217 Intermediate Similarity NPC31896
0.7119 Intermediate Similarity NPC480556
0.7037 Intermediate Similarity NPC475351
0.7027 Intermediate Similarity NPC480555
0.7027 Intermediate Similarity NPC150372
0.6983 Remote Similarity NPC477811
0.6944 Remote Similarity NPC113044
0.6944 Remote Similarity NPC283829
0.6944 Remote Similarity NPC161676
0.686 Remote Similarity NPC477808
0.6807 Remote Similarity NPC470866
0.6803 Remote Similarity NPC210569
0.6757 Remote Similarity NPC470433
0.6757 Remote Similarity NPC46190
0.6757 Remote Similarity NPC171073
0.6724 Remote Similarity NPC232611
0.6699 Remote Similarity NPC181845
0.6695 Remote Similarity NPC480553
0.6637 Remote Similarity NPC6806
0.6636 Remote Similarity NPC14704
0.6606 Remote Similarity NPC470432
0.6606 Remote Similarity NPC230507
0.6525 Remote Similarity NPC249265
0.6525 Remote Similarity NPC480554
0.6522 Remote Similarity NPC97700
0.6522 Remote Similarity NPC30856
0.6508 Remote Similarity NPC305771
0.6508 Remote Similarity NPC94072
0.6508 Remote Similarity NPC169816
0.6491 Remote Similarity NPC51172
0.6491 Remote Similarity NPC49032
0.641 Remote Similarity NPC269297
0.641 Remote Similarity NPC222202
0.6389 Remote Similarity NPC206003
0.6389 Remote Similarity NPC473610
0.6387 Remote Similarity NPC470864
0.6372 Remote Similarity NPC473601
0.6293 Remote Similarity NPC150057
0.6293 Remote Similarity NPC147753
0.627 Remote Similarity NPC15918
0.6261 Remote Similarity NPC248746
0.6261 Remote Similarity NPC477809
0.6186 Remote Similarity NPC475319
0.6154 Remote Similarity NPC475182
0.6148 Remote Similarity NPC132080
0.6124 Remote Similarity NPC244431
0.6111 Remote Similarity NPC224314
0.6102 Remote Similarity NPC73243
0.6102 Remote Similarity NPC244086
0.6102 Remote Similarity NPC84956
0.6087 Remote Similarity NPC98696
0.6068 Remote Similarity NPC42171
0.605 Remote Similarity NPC115165
0.6 Remote Similarity NPC247037
0.5966 Remote Similarity NPC294129
0.5935 Remote Similarity NPC470862
0.5913 Remote Similarity NPC305423
0.5902 Remote Similarity NPC232037
0.5897 Remote Similarity NPC475643
0.5882 Remote Similarity NPC151134
0.5877 Remote Similarity NPC125324
0.5859 Remote Similarity NPC477807
0.582 Remote Similarity NPC473518
0.582 Remote Similarity NPC13193
0.5806 Remote Similarity NPC23808
0.5806 Remote Similarity NPC87998
0.5781 Remote Similarity NPC248202
0.5769 Remote Similarity NPC79900
0.576 Remote Similarity NPC233433
0.5726 Remote Similarity NPC108072
0.569 Remote Similarity NPC141433
0.568 Remote Similarity NPC476112
0.568 Remote Similarity NPC83137
0.568 Remote Similarity NPC307534
0.5669 Remote Similarity NPC167183
0.5667 Remote Similarity NPC48886
0.5667 Remote Similarity NPC94881
0.563 Remote Similarity NPC485603
0.562 Remote Similarity NPC128572
0.5606 Remote Similarity NPC208832
0.5591 Remote Similarity NPC308140
0.5574 Remote Similarity NPC184617
0.5565 Remote Similarity NPC32361
0.554 Remote Similarity NPC329807
0.5532 Remote Similarity NPC481189
0.552 Remote Similarity NPC197003
0.5512 Remote Similarity NPC256983
0.5492 Remote Similarity NPC485604
0.5484 Remote Similarity NPC475550
0.547 Remote Similarity NPC94272
0.547 Remote Similarity NPC6295
0.5455 Remote Similarity NPC220836
0.5447 Remote Similarity NPC98018
0.5447 Remote Similarity NPC284104
0.5447 Remote Similarity NPC103616
0.5447 Remote Similarity NPC475247
0.5417 Remote Similarity NPC40440
0.5417 Remote Similarity NPC486388
0.5385 Remote Similarity NPC329727
0.5373 Remote Similarity NPC32707
0.536 Remote Similarity NPC486386
0.5351 Remote Similarity NPC477451
0.5339 Remote Similarity NPC306991
0.5333 Remote Similarity NPC485605
0.5304 Remote Similarity NPC250393
0.5294 Remote Similarity NPC70204
0.5285 Remote Similarity NPC249553
0.5285 Remote Similarity NPC471464
0.5285 Remote Similarity NPC124677
0.5285 Remote Similarity NPC182900
0.5276 Remote Similarity NPC254255
0.5268 Remote Similarity NPC485594
0.525 Remote Similarity NPC160426
0.5245 Remote Similarity NPC329820
0.5227 Remote Similarity NPC94086
0.5227 Remote Similarity NPC190939
0.5227 Remote Similarity NPC473817
0.5214 Remote Similarity NPC19400
0.5197 Remote Similarity NPC475625
0.5175 Remote Similarity NPC297348
0.5175 Remote Similarity NPC249204
0.5175 Remote Similarity NPC48339
0.5175 Remote Similarity NPC141769
0.5175 Remote Similarity NPC477547
0.5164 Remote Similarity NPC42482
0.5154 Remote Similarity NPC84111
0.5154 Remote Similarity NPC287483
0.5154 Remote Similarity NPC470865
0.5152 Remote Similarity NPC470867
0.5149 Remote Similarity NPC473505
0.5106 Remote Similarity NPC330026
0.5085 Remote Similarity NPC306131
0.5085 Remote Similarity NPC211354
0.5085 Remote Similarity NPC200802
0.5085 Remote Similarity NPC107188
0.5083 Remote Similarity NPC485595
0.5079 Remote Similarity NPC308459
0.5043 Remote Similarity NPC325828
0.5043 Remote Similarity NPC177834
0.5039 Remote Similarity NPC51520
0.5039 Remote Similarity NPC303069

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC47529 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
0.6293 Remote Similarity NPD8450 Suspended
0.5043 Remote Similarity NPD8171 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