Natural Product: NPC309557

Natural Product IDNPC309557
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 DDMBYMQDYQAZRZ-RKQHYHRCSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 21591970
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 DDMBYMQDYQAZRZ-RKQHYHRCSA-N
Standard InCHI InChI=1S/C14H18O8/c1-6(16)7-2-3-9(8(17)4-7)21-14-13(20)12(19)11(18)10(5-15)22-14/h2-4,10-15,17-20H,5H2,1H3/t10-,11-,12+,13-,14-/m1/s1
SMILES CC(=O)c1ccc(c(c1)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   314.1 Volume:   293.363
?
Van der Waals volume.
Dense:   1.071 LogP:   -0.913
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -0.261
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -0.951
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   4.0 Rigid Bonds:   13.0
TPSA:   136.68
?
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:   0.436 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.495 Fsp3:   0.5
MCE-18:   52.143
?
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:   0.534 Fluc inhibitor:   0.138
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.066
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.071
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.307 Promiscuous compounds:   0.384

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.068 MDCK Permeability:   -5.01
Pgp-inhibitor:   0.0 Pgp-substrate:   0.184
PAMPA:   0.986
?
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):   0.448
20% Bioavailability (F20%):   0.119 30% Bioavailability (F30%):   0.916
50% Bioavailability (F50%):   0.927

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.117 MRP1:   0.433
Plasma Protein Binding (PPB):   54.743% Volume Distribution (VD):   -0.372
Fu: 43.77%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.998
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.023
BSEP inhibitor:   0.0

ADMET: Metabolism

CYP1A2-inhibitor:   0.004 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.001 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.0
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.0
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.361
HLM stability:   0.13
?
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):  3.321 Half-life (T1/2):  3.072

ADMET: Toxicity

hERG Blockers:  0.022 hERG Blockers (10um):  0.11
Human Hepatotoxicity (H-HT):  0.644 Drug-induced Liver Injury (DILI):  0.714
AMES Toxicity:  0.869 Rat Oral Acute Toxicity:  0.022
Maximum Recommended Daily Dose:  0.013 Skin Sensitization:  0.99
Carcinogencity:  0.297 Eye Corrosion:  0.002
Eye Irritation:  0.702 Respiratory Toxicity:  0.035
Drug-induced Neurotoxicity:  0.018 Ototoxicity:  0.881
Hematotoxicity:  0.453 Drug-induced Nephrotoxicity:  0.538
Genotoxicity:  0.371 RPMI-8226 Immunitoxicity:  0.11
A549 Cytotoxicity:  0.128 Hek293 Cytotoxicity:  0.124
BCF:   0.268
?
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:   2.321
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   3.82
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   2.975
?
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
NPO2421 Picea glauca Species Pinaceae Eukaryota n.a. n.a. n.a. PMID[18636777]
NPO691 Tarchonanthus camphoratus Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[29244495]
NPO284 Albizia procera Species Fabaceae Eukaryota Bark n.a. n.a. PMID[30520635]
NPO1539 Artemisia giraldii Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[36364129]
NPO1539 Artemisia giraldii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO19432 Millettia pinnata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3963 Hortonia floribunda Species Monimiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO691 Tarchonanthus camphoratus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO4421 Penicillium cyclopium Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5981 Achlys triphylla Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7770 Lactuca laciniata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5588 Bursera tonkinensis Species Burseraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3415 Perymenium mendezii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO3255 Lampranthus sociorum Species Aizoaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2421 Picea glauca Species Pinaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO284 Albizia procera Species Fabaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO5588 Bursera tonkinensis Species Burseraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7155 Cypripedium calceolus Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7770 Lactuca laciniata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO99 Artemisia porrecta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO99 Artemisia porrecta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19432 Millettia pinnata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO5588 Bursera tonkinensis Species Burseraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7770 Lactuca laciniata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7155 Cypripedium calceolus Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7155 Cypripedium calceolus Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO855 Elymnias thryallis Species Nymphalidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7464 Uruparia lanosa n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO4421 Penicillium cyclopium Species Aspergillaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5981 Achlys triphylla Species Berberidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3963 Hortonia floribunda Species Monimiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO284 Albizia procera Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4952 Pertusaria amara Species Pertusariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3415 Perymenium mendezii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19432 Millettia pinnata Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7616 Melanargia galathea Species Nymphalidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3263 Thea sasanqua n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO99 Artemisia porrecta Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO691 Tarchonanthus camphoratus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5588 Bursera tonkinensis Species Burseraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7155 Cypripedium calceolus Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2421 Picea glauca Species Pinaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6844 Bulbophyllum protractum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3255 Lampranthus sociorum Species Aizoaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2963 Diospyros glaucifolia Species Ebenaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4117 Nauclea rhynchophylla Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15597 Calystegia pubescens Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29287 Alectoria ochroleuca Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1539 Artemisia giraldii Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7770 Lactuca laciniata Species Asteraceae 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 NPC309557 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
0.7358 Intermediate Similarity NPC205054
0.7358 Intermediate Similarity NPC19470
0.7222 Intermediate Similarity NPC481303
0.7143 Intermediate Similarity NPC294470
0.6667 Remote Similarity NPC9248
0.6552 Remote Similarity NPC59324
0.6441 Remote Similarity NPC100389
0.6316 Remote Similarity NPC210015
0.623 Remote Similarity NPC186418
0.623 Remote Similarity NPC202700
0.6032 Remote Similarity NPC106944
0.5926 Remote Similarity NPC60589
0.5926 Remote Similarity NPC469708
0.5893 Remote Similarity NPC214454
0.5862 Remote Similarity NPC23084
0.5846 Remote Similarity NPC116229
0.5833 Remote Similarity NPC25292
0.5806 Remote Similarity NPC174377
0.5789 Remote Similarity NPC310661
0.5769 Remote Similarity NPC212729
0.5769 Remote Similarity NPC142319
0.5769 Remote Similarity NPC604498
0.5714 Remote Similarity NPC221090
0.569 Remote Similarity NPC218685
0.5672 Remote Similarity NPC191046
0.5667 Remote Similarity NPC105827
0.566 Remote Similarity NPC269242
0.566 Remote Similarity NPC484157
0.5614 Remote Similarity NPC166168
0.56 Remote Similarity NPC228907
0.5588 Remote Similarity NPC72249
0.5556 Remote Similarity NPC192810
0.5556 Remote Similarity NPC469661
0.5556 Remote Similarity NPC65530
0.5538 Remote Similarity NPC98777
0.5538 Remote Similarity NPC189115
0.5536 Remote Similarity NPC200092
0.5536 Remote Similarity NPC12308
0.5517 Remote Similarity NPC40377
0.5517 Remote Similarity NPC9912
0.5507 Remote Similarity NPC310064
0.55 Remote Similarity NPC26080
0.55 Remote Similarity NPC165686
0.5484 Remote Similarity NPC97326
0.5429 Remote Similarity NPC232228
0.5385 Remote Similarity NPC474044
0.5362 Remote Similarity NPC488085
0.5357 Remote Similarity NPC609376
0.5333 Remote Similarity NPC270849
0.5323 Remote Similarity NPC222455
0.5323 Remote Similarity NPC106025
0.5323 Remote Similarity NPC599943
0.5294 Remote Similarity NPC88043
0.5286 Remote Similarity NPC147596
0.5263 Remote Similarity NPC226712
0.5263 Remote Similarity NPC608788
0.5238 Remote Similarity NPC473045
0.5224 Remote Similarity NPC177742
0.5217 Remote Similarity NPC45400
0.5179 Remote Similarity NPC152722
0.5172 Remote Similarity NPC80098
0.5172 Remote Similarity NPC145900
0.5156 Remote Similarity NPC478871
0.5156 Remote Similarity NPC190714
0.5156 Remote Similarity NPC478870
0.5156 Remote Similarity NPC199335
0.5156 Remote Similarity NPC478872
0.5156 Remote Similarity NPC478873
0.5156 Remote Similarity NPC477240
0.5152 Remote Similarity NPC212670
0.5152 Remote Similarity NPC216752
0.5152 Remote Similarity NPC206264
0.5147 Remote Similarity NPC165720
0.5139 Remote Similarity NPC5778
0.5085 Remote Similarity NPC166040
0.5085 Remote Similarity NPC604209
0.5082 Remote Similarity NPC472024
0.5082 Remote Similarity NPC604356
0.5077 Remote Similarity NPC294166
0.5077 Remote Similarity NPC190217
0.5077 Remote Similarity NPC252169
0.5077 Remote Similarity NPC115022
0.5077 Remote Similarity NPC611586
0.5075 Remote Similarity NPC212770
0.5075 Remote Similarity NPC475084
0.507 Remote Similarity NPC279298

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC309557 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
0.5263 Remote Similarity NPD1091 Pre-clinical
0.5152 Remote Similarity NPD1653 Approved

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