Natural Product: NPC50855

Natural Product IDNPC50855
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 GUBGYTABKSRVRQ-GFVAERMHSA-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:0002207] O-glycosyl 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 GUBGYTABKSRVRQ-GFVAERMHSA-N
Standard InCHI InChI=1S/C12H22O11/c13-1-3-5(15)6(16)9(19)12(22-3)23-10-4(2-14)21-11(20)8(18)7(10)17/h3-20H,1-2H2/t3-,4-,5+,6+,7-,8-,9+,10+,11-,12-/m0/s1
SMILES C([C@H]1[C@H]([C@H]([C@H]([C@@H](O1)O[C@@H]1[C@H](CO)O[C@@H]([C@H]([C@@H]1O)O)O)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   342.12 Volume:   295.688
?
Van der Waals volume.
Dense:   1.157 LogP:   -2.541
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -2.001
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -0.119
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   12.0
TPSA:   189.53
?
Topological Polar Surface Area.
 H-Bond Acceptor:   11.0
H-Bond Donor:   8.0 Rings:   2.0
Heavy Atoms:   11.0

MedChem Properties

QED Drug-Likeness Score:   0.243 GASA:   1.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.282 Fsp3:   1.0
MCE-18:   45.333
?
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:   Rejected
Golden Triangle Rule:   Accepted BMS Rule:   1
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.183 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.042
?
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:   0.505 Promiscuous compounds:   0.018

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.827 MDCK Permeability:   -4.985
Pgp-inhibitor:   0.0 Pgp-substrate:   0.918
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):   0.986
20% Bioavailability (F20%):   0.833 30% Bioavailability (F30%):   0.984
50% Bioavailability (F50%):   0.995

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.0 MRP1:   0.089
Plasma Protein Binding (PPB):   22.989% Volume Distribution (VD):   -0.616
Fu: 77.712%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.588
OATP1B3 inhibitor:   0.654 BCRP inhibitor:   0.002
BSEP inhibitor:   0.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.048 CYP2C9-substrate:   0.001
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.002
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.95
HLM stability:   0.051
?
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):  0.957 Half-life (T1/2):  2.682

ADMET: Toxicity

hERG Blockers:  0.004 hERG Blockers (10um):  0.063
Human Hepatotoxicity (H-HT):  0.579 Drug-induced Liver Injury (DILI):  0.775
AMES Toxicity:  0.938 Rat Oral Acute Toxicity:  0.044
Maximum Recommended Daily Dose:  0.008 Skin Sensitization:  1.0
Carcinogencity:  0.065 Eye Corrosion:  0.001
Eye Irritation:  0.776 Respiratory Toxicity:  0.134
Drug-induced Neurotoxicity:  0.031 Ototoxicity:  0.97
Hematotoxicity:  0.685 Drug-induced Nephrotoxicity:  0.921
Genotoxicity:  0.253 RPMI-8226 Immunitoxicity:  0.154
A549 Cytotoxicity:  0.162 Hek293 Cytotoxicity:  0.053
BCF:   0.113
?
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:   1.414
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   2.711
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   2.007
?
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
NPO3762 Amentotaxus argotaenia Species Taxaceae Eukaryota Leaves; Twigs n.a. n.a. PMID[32633512]
NPO822 Cressa cretica Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11832 Pinus banksiana Species Pinaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4144 Scutia buxifolia Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1313 Aplophyllum bungei n.a. n.a. n.a. n.a. n.a. n.a. Database[COCONUT]
NPO316 Fuligo aurea Species Physaraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2559 Mesua myrtifolia Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6796 Planchonella anteridifera Species Sapotaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6040 Svenzea zeai Species Dictyonellidae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO6194 Thalictrum pedunculatum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1191 Castanea mollissima Species Fagaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3102 Arachniodes exilis Species Dryopteridaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9522 Pericopsis angolensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9311 Parkia clappertoniana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9051 Delesseria sanguinea Species Delesseriaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO1191 Castanea mollissima Species Fagaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4144 Scutia buxifolia Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12322 Amomum krervanh Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1191 Castanea mollissima Species Fagaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4144 Scutia buxifolia Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9522 Pericopsis angolensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3102 Arachniodes exilis Species Dryopteridaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1191 Castanea mollissima Species Fagaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12322 Amomum krervanh Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO12895 Polypodiodes niponica Species Polypodiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2559 Mesua myrtifolia Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9051 Delesseria sanguinea Species Delesseriaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3102 Arachniodes exilis Species Dryopteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO822 Cressa cretica Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3762 Amentotaxus argotaenia Species Taxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12322 Amomum krervanh Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5205 Gymnoascus reesii Species Gymnoascaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9311 Parkia clappertoniana Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4144 Scutia buxifolia Species Rhamnaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10588 Diploschistes violarius Species Graphidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO316 Fuligo aurea Species Physaraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9522 Pericopsis angolensis Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11832 Pinus banksiana Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6194 Thalictrum pedunculatum Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1191 Castanea mollissima Species Fagaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6796 Planchonella anteridifera Species Sapotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6040 Svenzea zeai Species Dictyonellidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1313 Aplophyllum bungei n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO10177 Eria linearifolia Species Orchidaceae 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 NPC50855 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
1.0 High Similarity NPC246558
1.0 High Similarity NPC67660
1.0 High Similarity NPC165198
1.0 High Similarity NPC209753
1.0 High Similarity NPC58629
0.8947 High Similarity NPC317023
0.8947 High Similarity NPC489878
0.6111 Remote Similarity NPC23134
0.5455 Remote Similarity NPC323361
0.5435 Remote Similarity NPC89145
0.5435 Remote Similarity NPC157514
0.5435 Remote Similarity NPC322314
0.5435 Remote Similarity NPC269166
0.5405 Remote Similarity NPC42503
0.5405 Remote Similarity NPC282143
0.5405 Remote Similarity NPC107914
0.5405 Remote Similarity NPC242073
0.5405 Remote Similarity NPC299781
0.5405 Remote Similarity NPC157193
0.5405 Remote Similarity NPC608193
0.5208 Remote Similarity NPC604425
0.5102 Remote Similarity NPC477750
0.5102 Remote Similarity NPC477763
0.5102 Remote Similarity NPC477757
0.5102 Remote Similarity NPC477762
0.5102 Remote Similarity NPC477755
0.5102 Remote Similarity NPC477753

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC50855 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
1.0 High Similarity NPD888 Phase 3
1.0 High Similarity NPD890 Clinical (unspecified phase)
1.0 High Similarity NPD891 Phase 3
1.0 High Similarity NPD892 Phase 3
1.0 High Similarity NPD893 Approved
0.5455 Remote Similarity NPD889 Approved
0.5455 Remote Similarity NPD894 Phase 4
0.5366 Remote Similarity NPD905 Phase 4

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