Natural Product: NPC307473

Natural Product IDNPC307473
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 SQRUWMQAWMLKPR-UHFFFAOYSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 4480901
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0001540] Monosaccharides
            • [CHEMONTID:0001498] Hexoses

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 SQRUWMQAWMLKPR-UHFFFAOYSA-N
Standard InCHI InChI=1S/C11H18O8/c1-5(2-3-12)10(17)19-11-9(16)8(15)7(14)6(4-13)18-11/h6-9,11-16H,1-4H2
SMILES C=C(CCO)C(=O)OC1C(C(C(C(CO)O1)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   278.1 Volume:   255.305
?
Van der Waals volume.
Dense:   1.089 LogP:   -1.278
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -0.655
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -0.554
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   6.0 Rigid Bonds:   8.0
TPSA:   136.68
?
Topological Polar Surface Area.
 H-Bond Acceptor:   8.0
H-Bond Donor:   5.0 Rings:   1.0
Heavy Atoms:   8.0

MedChem Properties

QED Drug-Likeness Score:   0.27 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.012 Fsp3:   0.727
MCE-18:   25.263
?
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:   1
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.008 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.034
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.002
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.347 Promiscuous compounds:   0.128

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.087 MDCK Permeability:   -5.114
Pgp-inhibitor:   0.0 Pgp-substrate:   0.327
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):   0.996
20% Bioavailability (F20%):   0.885 30% Bioavailability (F30%):   0.997
50% Bioavailability (F50%):   0.986

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.098 MRP1:   0.5
Plasma Protein Binding (PPB):   33.507% Volume Distribution (VD):   -0.502
Fu: 74.762%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.012
OATP1B3 inhibitor:   0.856 BCRP inhibitor:   0.026
BSEP inhibitor:   0.025

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.001 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.968 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.001 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.026 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.016
HLM stability:   0.004
?
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):  3.203 Half-life (T1/2):  1.851

ADMET: Toxicity

hERG Blockers:  0.015 hERG Blockers (10um):  0.158
Human Hepatotoxicity (H-HT):  0.499 Drug-induced Liver Injury (DILI):  0.135
AMES Toxicity:  0.481 Rat Oral Acute Toxicity:  0.087
Maximum Recommended Daily Dose:  0.035 Skin Sensitization:  0.65
Carcinogencity:  0.28 Eye Corrosion:  0.004
Eye Irritation:  0.63 Respiratory Toxicity:  0.064
Drug-induced Neurotoxicity:  0.151 Ototoxicity:  0.909
Hematotoxicity:  0.154 Drug-induced Nephrotoxicity:  0.207
Genotoxicity:  0.038 RPMI-8226 Immunitoxicity:  0.04
A549 Cytotoxicity:  0.007 Hek293 Cytotoxicity:  0.104
BCF:   0.118
?
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:   1.486
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   2.961
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   2.02
?
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
NPO12721 Liriodendron tulipifera Species Magnoliaceae Eukaryota n.a. n.a. n.a. PMID[23501116]
NPO11984 Tulipa gesneriana Species Liliaceae Eukaryota n.a. n.a. n.a. PMID[25126881]
NPO12721 Liriodendron tulipifera Species Magnoliaceae Eukaryota n.a. n.a. n.a. PMID[31444719]
NPO11984 Tulipa gesneriana Species Liliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12721 Liriodendron tulipifera Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO12721 Liriodendron tulipifera Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11984 Tulipa gesneriana Species Liliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11984 Tulipa gesneriana Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12721 Liriodendron tulipifera Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12721 Liriodendron tulipifera Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11984 Tulipa gesneriana Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12721 Liriodendron tulipifera Species Magnoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11984 Tulipa gesneriana Species Liliaceae 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 NPC307473 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 NPC603514
0.5957 Remote Similarity NPC482640
0.58 Remote Similarity NPC180071
0.549 Remote Similarity NPC119058
0.5455 Remote Similarity NPC155457
0.5455 Remote Similarity NPC268243
0.5263 Remote Similarity NPC42503
0.5263 Remote Similarity NPC282143
0.5263 Remote Similarity NPC107914
0.5263 Remote Similarity NPC242073
0.5263 Remote Similarity NPC299781
0.5263 Remote Similarity NPC157193
0.5263 Remote Similarity NPC608193
0.525 Remote Similarity NPC124963
0.5128 Remote Similarity NPC23134
0.5122 Remote Similarity NPC326533
0.5091 Remote Similarity NPC143446

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC307473 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
NPD

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