Natural Product: NPC100179

Natural Product IDNPC100179
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 ZZDVZVBAZHPHLY-ZQNQSHIBSA-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 ZZDVZVBAZHPHLY-ZQNQSHIBSA-N
Standard InCHI InChI=1S/C15H22O8/c1-21-10-6-8(4-5-16)2-3-9(10)22-15-14(20)13(19)12(18)11(7-17)23-15/h2-3,6,11-20H,4-5,7H2,1H3/t11-,12+,13-,14+,15-/m0/s1
SMILES COc1cc(ccc1O[C@@H]1[C@@H]([C@H]([C@@H]([C@H](CO)O1)O)O)O)CCO

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   330.13 Volume:   313.296
?
Van der Waals volume.
Dense:   1.054 LogP:   -0.914
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -0.427
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -0.823
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   6.0 Rigid Bonds:   12.0
TPSA:   128.84
?
Topological Polar Surface Area.
 H-Bond Acceptor:   8.0
H-Bond Donor:   5.0 Rings:   2.0
Heavy Atoms:   8.0

MedChem Properties

QED Drug-Likeness Score:   0.422 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.443 Fsp3:   0.6
MCE-18:   47.833
?
MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
 Lipinski Rule-of-5:   Rejected
Pfizer Rule:   Rejected GSK Rule:   Rejected
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.526 Fluc inhibitor:   0.021
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.103
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.059
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.218 Promiscuous compounds:   0.029

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.939 MDCK Permeability:   -5.171
Pgp-inhibitor:   0.001 Pgp-substrate:   0.943
PAMPA:   0.995
?
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):   0.588
20% Bioavailability (F20%):   0.171 30% Bioavailability (F30%):   0.144
50% Bioavailability (F50%):   0.929

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.004 MRP1:   0.154
Plasma Protein Binding (PPB):   41.551% Volume Distribution (VD):   -0.349
Fu: 58.181%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.87
OATP1B3 inhibitor:   0.865 BCRP inhibitor:   0.27
BSEP inhibitor:   0.658

ADMET: Metabolism

CYP1A2-inhibitor:   0.752 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.015 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.021 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.002
CYP3A4-inhibitor:   0.021 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.035
HLM stability:   0.036
?
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):  1.942 Half-life (T1/2):  3.087

ADMET: Toxicity

hERG Blockers:  0.03 hERG Blockers (10um):  0.238
Human Hepatotoxicity (H-HT):  0.494 Drug-induced Liver Injury (DILI):  0.148
AMES Toxicity:  0.568 Rat Oral Acute Toxicity:  0.013
Maximum Recommended Daily Dose:  0.005 Skin Sensitization:  0.914
Carcinogencity:  0.13 Eye Corrosion:  0.001
Eye Irritation:  0.664 Respiratory Toxicity:  0.01
Drug-induced Neurotoxicity:  0.015 Ototoxicity:  0.959
Hematotoxicity:  0.213 Drug-induced Nephrotoxicity:  0.59
Genotoxicity:  0.004 RPMI-8226 Immunitoxicity:  0.077
A549 Cytotoxicity:  0.025 Hek293 Cytotoxicity:  0.044
BCF:   0.241
?
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:   2.339
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   3.836
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   2.967
?
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
NPO16066 Urtica cannabina Species Urticaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16066 Urtica cannabina Species Urticaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16066 Urtica cannabina Species Urticaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16066 Urtica cannabina Species Urticaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16066 Urtica cannabina Species Urticaceae 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 NPC100179 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
0.8235 Intermediate Similarity NPC472024
0.8235 Intermediate Similarity NPC270849
0.8077 Intermediate Similarity NPC26653
0.8077 Intermediate Similarity NPC80600
0.75 Intermediate Similarity NPC9912
0.7451 Intermediate Similarity NPC69513
0.7308 Intermediate Similarity NPC166040
0.6667 Remote Similarity NPC248355
0.6562 Remote Similarity NPC158635
0.6562 Remote Similarity NPC229882
0.6552 Remote Similarity NPC55040
0.6458 Remote Similarity NPC228907
0.6441 Remote Similarity NPC302378
0.6364 Remote Similarity NPC227902
0.6269 Remote Similarity NPC471063
0.625 Remote Similarity NPC215833
0.623 Remote Similarity NPC276753
0.623 Remote Similarity NPC205796
0.6226 Remote Similarity NPC25817
0.6129 Remote Similarity NPC37468
0.6129 Remote Similarity NPC246947
0.6129 Remote Similarity NPC604095
0.6111 Remote Similarity NPC60589
0.6111 Remote Similarity NPC469708
0.6102 Remote Similarity NPC479029
0.597 Remote Similarity NPC61594
0.5882 Remote Similarity NPC56735
0.5833 Remote Similarity NPC299706
0.5833 Remote Similarity NPC245615
0.5833 Remote Similarity NPC115466
0.5833 Remote Similarity NPC39657
0.5833 Remote Similarity NPC61604
0.5818 Remote Similarity NPC299144
0.5775 Remote Similarity NPC93924
0.5775 Remote Similarity NPC217635
0.5763 Remote Similarity NPC479028
0.5763 Remote Similarity NPC479031
0.5763 Remote Similarity NPC19470
0.5741 Remote Similarity NPC153149
0.5692 Remote Similarity NPC210192
0.5692 Remote Similarity NPC475096
0.5676 Remote Similarity NPC46092
0.5676 Remote Similarity NPC470950
0.5676 Remote Similarity NPC163635
0.566 Remote Similarity NPC276195
0.566 Remote Similarity NPC212729
0.566 Remote Similarity NPC604498
0.56 Remote Similarity NPC486548
0.56 Remote Similarity NPC129417
0.56 Remote Similarity NPC283995
0.5556 Remote Similarity NPC217854
0.5556 Remote Similarity NPC269242
0.5536 Remote Similarity NPC609376
0.5522 Remote Similarity NPC148273
0.5517 Remote Similarity NPC48863
0.5517 Remote Similarity NPC251981
0.5517 Remote Similarity NPC13745
0.5507 Remote Similarity NPC286235
0.5455 Remote Similarity NPC189115
0.5455 Remote Similarity NPC294470
0.5439 Remote Similarity NPC226712
0.5439 Remote Similarity NPC608788
0.5429 Remote Similarity NPC38041
0.5429 Remote Similarity NPC18979
0.5429 Remote Similarity NPC22150
0.5429 Remote Similarity NPC279298
0.541 Remote Similarity NPC210478
0.5357 Remote Similarity NPC152722
0.5345 Remote Similarity NPC145900
0.5333 Remote Similarity NPC218685
0.5333 Remote Similarity NPC49074
0.5263 Remote Similarity NPC185307
0.5254 Remote Similarity NPC610709
0.5246 Remote Similarity NPC162093
0.5238 Remote Similarity NPC104167
0.5231 Remote Similarity NPC294166
0.5231 Remote Similarity NPC115022
0.5211 Remote Similarity NPC476411
0.5195 Remote Similarity NPC486549
0.5195 Remote Similarity NPC470235
0.5179 Remote Similarity NPC192810
0.5172 Remote Similarity NPC200092
0.5161 Remote Similarity NPC210015
0.5156 Remote Similarity NPC247146
0.5152 Remote Similarity NPC479030
0.5128 Remote Similarity NPC486546
0.5091 Remote Similarity NPC142319
0.5085 Remote Similarity NPC221090
0.5085 Remote Similarity NPC80098
0.5072 Remote Similarity NPC479447
0.5067 Remote Similarity NPC43508

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC100179 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
0.5439 Remote Similarity NPD1091 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