Natural Product: NPC482735

Natural Product IDNPC482735
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
CWRRYAWFDXCSDM-NHODMXMXSA-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]

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 CWRRYAWFDXCSDM-NHODMXMXSA-N
Standard InCHI InChI=1S/C50H74O22/c1-19-27(53)28(54)33(59)41(66-19)71-37-32(58)30(56)35(40(62)63)70-43(37)72-36-31(57)29(55)34(39(60)61)69-42(36)68-25-11-12-48(7)24(45(25,3)4)10-13-50(9)38(48)23(52)16-21-22-17-46(5,44(64)65)18-26(67-20(2)51)47(22,6)14-15-49(21,50)8/h16,19,22,24-38,41-43,53-59H,10-15,17-18H2,1-9H3,(H,60,61)(H,62,63)(H,64,65)/t19-,22+,24-,25-,26+,27-,28+,29+,30-,31+,32-,33+,34+,35-,36-,37+,38+,41-,42-,43-,46+,47+,48-,49+,50+/m1/s1
SMILES C[C@@H]1[C@H]([C@@H]([C@@H]([C@H](O1)O[C@H]1[C@@H]([C@H]([C@H](C(=O)O)O[C@@H]1O[C@@H]1[C@H]([C@@H]([C@@H](C(=O)O)O[C@H]1O[C@@H]1CC[C@]2(C)[C@H](CC[C@@]3(C)[C@H]2C(=O)C=C2[C@@H]4C[C@@](C)(C[C@@H]([C@@]4(C)CC[C@]32C)OC(=O)C)C(=O)O)C1(C)C)O)O)O)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   1026.47 Volume:   982.47
?
Van der Waals volume.
Dense:   1.045 LogP:   1.206
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.712
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -3.931
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   11.0 Rigid Bonds:   49.0
TPSA:   352.26
?
Topological Polar Surface Area.
H-Bond Acceptor:   22.0
H-Bond Donor:   10.0 Rings:   8.0
Heavy Atoms:   22.0

MedChem Properties

QED Drug-Likeness Score:   0.106 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   6.618 Fsp3:   0.86
MCE-18:   185.72
?
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:   0.752 Fluc inhibitor:   0.003
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.049
?
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:   0.237 Promiscuous compounds:   0.325

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.126 MDCK Permeability:   -5.139
Pgp-inhibitor:   0.0 Pgp-substrate:   0.057
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):   0.037
20% Bioavailability (F20%):   0.025 30% Bioavailability (F30%):   0.023
50% Bioavailability (F50%):   0.891

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.975
Plasma Protein Binding (PPB):   53.46% Volume Distribution (VD):   -0.552
Fu: 31.81%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   0.995
OATP1B3 inhibitor:   0.097 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:   1.0 CYP3A4-substrate:   0.956
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.951
HLM stability:   0.0
?
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):  -0.175 Half-life (T1/2):  4.661

ADMET: Toxicity

hERG Blockers:  0.0 hERG Blockers (10um):  0.0
Human Hepatotoxicity (H-HT):  0.497 Drug-induced Liver Injury (DILI):  0.99
AMES Toxicity:  0.101 Rat Oral Acute Toxicity:  0.011
Maximum Recommended Daily Dose:  0.004 Skin Sensitization:  1.0
Carcinogencity:  0.006 Eye Corrosion:  0.0
Eye Irritation:  0.002 Respiratory Toxicity:  0.005
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  0.993
Hematotoxicity:  0.25 Drug-induced Nephrotoxicity:  0.999
Genotoxicity:  0.933 RPMI-8226 Immunitoxicity:  0.146
A549 Cytotoxicity:  0.007 Hek293 Cytotoxicity:  0.006
BCF:   0.34
?
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:   3.542
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   5.434
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   4.313
?
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
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s11164-015-2099-x]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. DOI[10.1134/S1021443711030101]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. root n.a. PMID[16441081]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[16675659]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. root n.a. PMID[22074222]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[22074222]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. rhizome n.a. PMID[23867078]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. root n.a. PMID[23867078]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[24479468]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota roots n.a. n.a. PMID[24957203]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[25445757]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[25744461]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[26841168]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[32196343]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7154 Glycyrrhiza uralensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7154 Glycyrrhiza uralensis 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
NPT742 Organism Influenza A virus Influenza A virus Activity = 47.0 % PMID[26841168]
NPT742 Organism Influenza A virus Influenza A virus IC50 = 39600.0 nM PMID[26841168]

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 NPC482735 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
0.93 High Similarity NPC482739
0.9208 High Similarity NPC482736
0.9208 High Similarity NPC482738
0.898 High Similarity NPC482737
0.8866 High Similarity NPC482734
0.8866 High Similarity NPC182342
0.8866 High Similarity NPC482727
0.8866 High Similarity NPC471964
0.8039 Intermediate Similarity NPC482755
0.75 Intermediate Similarity NPC482722
0.75 Intermediate Similarity NPC471963
0.7196 Intermediate Similarity NPC262199
0.717 Intermediate Similarity NPC482744
0.7143 Intermediate Similarity NPC471965
0.7143 Intermediate Similarity NPC482749
0.713 Intermediate Similarity NPC482740
0.7117 Intermediate Similarity NPC471962
0.7115 Intermediate Similarity NPC482747
0.7115 Intermediate Similarity NPC202666
0.7115 Intermediate Similarity NPC471961
0.7115 Intermediate Similarity NPC242015
0.6981 Remote Similarity NPC285091
0.6509 Remote Similarity NPC482750
0.6422 Remote Similarity NPC482741
0.6422 Remote Similarity NPC482745
0.6422 Remote Similarity NPC482743
0.6422 Remote Similarity NPC146753
0.633 Remote Similarity NPC482717
0.6306 Remote Similarity NPC14617
0.625 Remote Similarity NPC482729
0.625 Remote Similarity NPC482742
0.6228 Remote Similarity NPC247315
0.6228 Remote Similarity NPC482728
0.619 Remote Similarity NPC482752
0.5849 Remote Similarity NPC471967
0.5752 Remote Similarity NPC482746
0.5625 Remote Similarity NPC309780
0.5378 Remote Similarity NPC131469
0.5372 Remote Similarity NPC477075
0.5372 Remote Similarity NPC477079
0.5333 Remote Similarity NPC95437
0.5328 Remote Similarity NPC477077
0.5328 Remote Similarity NPC477078
0.5289 Remote Similarity NPC114692
0.5248 Remote Similarity NPC74751
0.5246 Remote Similarity NPC477076
0.521 Remote Similarity NPC251768
0.5203 Remote Similarity NPC187618
0.5159 Remote Similarity NPC313110
0.5128 Remote Similarity NPC472949
0.5082 Remote Similarity NPC64715
0.5081 Remote Similarity NPC120116
0.5043 Remote Similarity NPC275343
0.5043 Remote Similarity NPC482748
0.5038 Remote Similarity NPC258617

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC482735 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
0.7115 Intermediate Similarity NPD8328 Phase 2
0.5248 Remote Similarity NPD7748 Pre-clinical

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