Natural Product: NPC484157

Natural Product IDNPC484157
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 ALFLBPNQQXFFGM-GPTQDWHKSA-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:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0002105] Glycosyl compounds
            • [CHEMONTID:0004165] Phenolic glycosides

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 ALFLBPNQQXFFGM-GPTQDWHKSA-N
Standard InCHI InChI=1S/C12H16O9/c13-3-7-8(17)9(18)10(19)12(20-7)21-11-5(15)1-4(14)2-6(11)16/h1-2,7-10,12-19H,3H2/t7-,8-,9+,10-,12+/m1/s1
SMILES c1c(cc(c(c1O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   304.08 Volume:   270.198
?
Van der Waals volume.
Dense:   1.125 LogP:   -1.227
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -0.572
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -0.873
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   3.0 Rigid Bonds:   12.0
TPSA:   160.07
?
Topological Polar Surface Area.
 H-Bond Acceptor:   9.0
H-Bond Donor:   7.0 Rings:   2.0
Heavy Atoms:   9.0

MedChem Properties

QED Drug-Likeness Score:   0.334 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.781 Fsp3:   0.5
MCE-18:   53.333
?
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:   1 PAINS Alert:   0
Colloidal aggregators:   0.546 Fluc inhibitor:   0.257
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.088
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.014
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.444 Promiscuous compounds:   0.647

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.53 MDCK Permeability:   -4.974
Pgp-inhibitor:   0.0 Pgp-substrate:   0.127
PAMPA:   0.96
?
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):   0.129
20% Bioavailability (F20%):   0.467 30% Bioavailability (F30%):   0.919
50% Bioavailability (F50%):   0.949

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.518 MRP1:   0.351
Plasma Protein Binding (PPB):   62.724% Volume Distribution (VD):   -0.252
Fu: 36.004%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.974
OATP1B3 inhibitor:   0.99 BCRP inhibitor:   0.28
BSEP inhibitor:   0.001

ADMET: Metabolism

CYP1A2-inhibitor:   0.14 CYP1A2-substrate:   0.006
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.024
CYP2C9-inhibitor:   0.715 CYP2C9-substrate:   0.246
CYP2D6-inhibitor:   0.463 CYP2D6-substrate:   0.041
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.712
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.895
HLM stability:   0.621
?
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):  3.902 Half-life (T1/2):  2.281

ADMET: Toxicity

hERG Blockers:  0.011 hERG Blockers (10um):  0.251
Human Hepatotoxicity (H-HT):  0.491 Drug-induced Liver Injury (DILI):  0.335
AMES Toxicity:  0.724 Rat Oral Acute Toxicity:  0.084
Maximum Recommended Daily Dose:  0.076 Skin Sensitization:  0.977
Carcinogencity:  0.103 Eye Corrosion:  0.004
Eye Irritation:  0.958 Respiratory Toxicity:  0.132
Drug-induced Neurotoxicity:  0.017 Ototoxicity:  0.693
Hematotoxicity:  0.064 Drug-induced Nephrotoxicity:  0.484
Genotoxicity:  0.398 RPMI-8226 Immunitoxicity:  0.147
A549 Cytotoxicity:  0.474 Hek293 Cytotoxicity:  0.28
BCF:   0.329
?
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:   1.876
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   3.039
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   2.273
?
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
NPO23736 Myrsine africana Species Primulaceae Eukaryota root n.a. n.a. PMID[2778455]
NPO23736 Myrsine africana Species Primulaceae Eukaryota n.a. n.a. n.a. PMID[29300477]
NPO23736 Myrsine africana Species Primulaceae Eukaryota n.a. fruit n.a. Database[Article]
NPO23736 Myrsine africana Species Primulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO23736 Myrsine africana Species Primulaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23736 Myrsine africana Species Primulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23736 Myrsine africana Species Primulaceae 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
NPT43 Individual protein Tyrosinase Agaricus bisporus IC50 = 410000.0 nM PMID[29300477]

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT35 Others n.a. n.a. IC50 = 3900.0 nM PMID[29300477]

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 NPC484157 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
0.6667 Remote Similarity NPC142319
0.66 Remote Similarity NPC310661
0.625 Remote Similarity NPC9248
0.625 Remote Similarity NPC152722
0.6136 Remote Similarity NPC228907
0.6042 Remote Similarity NPC192810
0.6 Remote Similarity NPC12308
0.5882 Remote Similarity NPC221090
0.5882 Remote Similarity NPC145900
0.5789 Remote Similarity NPC478871
0.5789 Remote Similarity NPC478870
0.5789 Remote Similarity NPC478872
0.5789 Remote Similarity NPC478873
0.5769 Remote Similarity NPC166168
0.569 Remote Similarity NPC252169
0.566 Remote Similarity NPC40377
0.5636 Remote Similarity NPC26080
0.5636 Remote Similarity NPC165686
0.5625 Remote Similarity NPC276195
0.5625 Remote Similarity NPC212729
0.5625 Remote Similarity NPC604498
0.5614 Remote Similarity NPC59324
0.5536 Remote Similarity NPC57751
0.551 Remote Similarity NPC217854
0.551 Remote Similarity NPC269242
0.5472 Remote Similarity NPC214454
0.5455 Remote Similarity NPC205054
0.5455 Remote Similarity NPC19470
0.5439 Remote Similarity NPC106025
0.5424 Remote Similarity NPC469661
0.5424 Remote Similarity NPC65530
0.5424 Remote Similarity NPC484156
0.54 Remote Similarity NPC153149
0.54 Remote Similarity NPC294470
0.5357 Remote Similarity NPC214910
0.5357 Remote Similarity NPC210015
0.5357 Remote Similarity NPC481303
0.5333 Remote Similarity NPC185778
0.5294 Remote Similarity NPC25817
0.5254 Remote Similarity NPC100389
0.5254 Remote Similarity NPC199335
0.5254 Remote Similarity NPC477240
0.5238 Remote Similarity NPC165720
0.5192 Remote Similarity NPC299144
0.5192 Remote Similarity NPC60589
0.5192 Remote Similarity NPC469708
0.5192 Remote Similarity NPC604439
0.5192 Remote Similarity NPC609376
0.5185 Remote Similarity NPC604209
0.5179 Remote Similarity NPC83975
0.5179 Remote Similarity NPC23084
0.5179 Remote Similarity NPC604356
0.5172 Remote Similarity NPC189589
0.5172 Remote Similarity NPC25292
0.5167 Remote Similarity NPC190217
0.5094 Remote Similarity NPC200092
0.5094 Remote Similarity NPC226712
0.5094 Remote Similarity NPC608788
0.5085 Remote Similarity NPC85799
0.5085 Remote Similarity NPC473045
0.5085 Remote Similarity NPC303422
0.5085 Remote Similarity NPC218003
0.5085 Remote Similarity NPC208769
0.5085 Remote Similarity NPC97326
0.5082 Remote Similarity NPC37074
0.5082 Remote Similarity NPC8497
0.5082 Remote Similarity NPC202700
0.5082 Remote Similarity NPC604095

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC484157 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
0.5094 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