Natural Product: NPC66968

Natural Product IDNPC66968
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 NUZMLNQKLRRREC-SSZWKKLZSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 158942
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 NUZMLNQKLRRREC-SSZWKKLZSA-N
Standard InCHI InChI=1S/C16H22O9/c1-7(18)8-4-9(22-2)15(10(5-8)23-3)25-16-14(21)13(20)12(19)11(6-17)24-16/h4-5,11-14,16-17,19-21H,6H2,1-3H3/t11-,12-,13+,14-,16+/m1/s1
SMILES CC(=O)c1cc(c(c(c1)OC)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)OC

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   358.13 Volume:   336.746
?
Van der Waals volume.
Dense:   1.064 LogP:   -0.689
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -0.198
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -1.093
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   6.0 Rigid Bonds:   13.0
TPSA:   134.91
?
Topological Polar Surface Area.
 H-Bond Acceptor:   9.0
H-Bond Donor:   4.0 Rings:   2.0
Heavy Atoms:   9.0

MedChem Properties

QED Drug-Likeness Score:   0.476 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   3.504 Fsp3:   0.562
MCE-18:   54.4
?
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:   0.586 Fluc inhibitor:   0.001
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.114
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.047
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.236 Promiscuous compounds:   0.451

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.449 MDCK Permeability:   -4.89
Pgp-inhibitor:   0.004 Pgp-substrate:   0.35
PAMPA:   0.718
?
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):   0.361
20% Bioavailability (F20%):   0.053 30% Bioavailability (F30%):   0.6
50% Bioavailability (F50%):   0.78

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.667 MRP1:   0.106
Plasma Protein Binding (PPB):   59.998% Volume Distribution (VD):   -0.237
Fu: 38.913%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.998
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.071
BSEP inhibitor:   0.021

ADMET: Metabolism

CYP1A2-inhibitor:   0.002 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.023 CYP2C19-substrate:   0.001
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.025
CYP3A4-inhibitor:   0.007 CYP3A4-substrate:   0.002
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.275
HLM stability:   0.147
?
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):  2.937 Half-life (T1/2):  3.115

ADMET: Toxicity

hERG Blockers:  0.028 hERG Blockers (10um):  0.115
Human Hepatotoxicity (H-HT):  0.681 Drug-induced Liver Injury (DILI):  0.803
AMES Toxicity:  0.856 Rat Oral Acute Toxicity:  0.027
Maximum Recommended Daily Dose:  0.032 Skin Sensitization:  0.972
Carcinogencity:  0.385 Eye Corrosion:  0.0
Eye Irritation:  0.185 Respiratory Toxicity:  0.028
Drug-induced Neurotoxicity:  0.069 Ototoxicity:  0.911
Hematotoxicity:  0.603 Drug-induced Nephrotoxicity:  0.705
Genotoxicity:  0.556 RPMI-8226 Immunitoxicity:  0.175
A549 Cytotoxicity:  0.152 Hek293 Cytotoxicity:  0.163
BCF:   0.246
?
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:   2.573
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   3.977
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.256
?
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
NPO11120 Brassica rapa Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[21448706]
NPO11120 Brassica rapa Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[21856162]
NPO11120 Brassica rapa Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[23001436]
NPO11120 Brassica rapa Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[24868877]
NPO11120 Brassica rapa Species Brassicaceae Eukaryota n.a. aerial part n.a. PMID[24919480]
NPO11120 Brassica rapa Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[38202700]
NPO11120 Brassica rapa Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO11120 Brassica rapa Species Brassicaceae Eukaryota n.a. n.a. Database[FooDB]
NPO11120 Brassica rapa Species Brassicaceae Eukaryota Oil n.a. n.a. Database[FooDB]
NPO11120 Brassica rapa Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11120 Brassica rapa Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11120 Brassica rapa Species Brassicaceae 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 NPC66968 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
0.75 Intermediate Similarity NPC299144
0.72 Intermediate Similarity NPC69513
0.7059 Intermediate Similarity NPC48863
0.7059 Intermediate Similarity NPC251981
0.7059 Intermediate Similarity NPC13745
0.6923 Remote Similarity NPC215833
0.6875 Remote Similarity NPC217854
0.6852 Remote Similarity NPC210478
0.6792 Remote Similarity NPC218685
0.6792 Remote Similarity NPC49074
0.6735 Remote Similarity NPC294470
0.6667 Remote Similarity NPC162093
0.66 Remote Similarity NPC152722
0.6364 Remote Similarity NPC23084
0.6327 Remote Similarity NPC276195
0.6316 Remote Similarity NPC95392
0.6316 Remote Similarity NPC84013
0.6316 Remote Similarity NPC55715
0.6316 Remote Similarity NPC35877
0.6207 Remote Similarity NPC232673
0.617 Remote Similarity NPC228907
0.614 Remote Similarity NPC479029
0.6111 Remote Similarity NPC166040
0.6111 Remote Similarity NPC95292
0.6102 Remote Similarity NPC470236
0.6078 Remote Similarity NPC153149
0.6071 Remote Similarity NPC270849
0.6071 Remote Similarity NPC205054
0.6066 Remote Similarity NPC474044
0.6038 Remote Similarity NPC608788
0.5968 Remote Similarity NPC475084
0.5965 Remote Similarity NPC26653
0.5962 Remote Similarity NPC25817
0.5902 Remote Similarity NPC479030
0.5849 Remote Similarity NPC609376
0.5806 Remote Similarity NPC146803
0.5789 Remote Similarity NPC472024
0.5781 Remote Similarity NPC479447
0.5781 Remote Similarity NPC148273
0.5758 Remote Similarity NPC61594
0.5741 Remote Similarity NPC226712
0.5714 Remote Similarity NPC9912
0.569 Remote Similarity NPC80600
0.5686 Remote Similarity NPC212729
0.5686 Remote Similarity NPC604498
0.5672 Remote Similarity NPC56735
0.5625 Remote Similarity NPC216129
0.5625 Remote Similarity NPC130449
0.5625 Remote Similarity NPC248132
0.5593 Remote Similarity NPC248355
0.5577 Remote Similarity NPC269242
0.5556 Remote Similarity NPC60589
0.5556 Remote Similarity NPC469708
0.5536 Remote Similarity NPC214454
0.5517 Remote Similarity NPC479028
0.5517 Remote Similarity NPC479031
0.55 Remote Similarity NPC106025
0.55 Remote Similarity NPC55040
0.5472 Remote Similarity NPC192810
0.5469 Remote Similarity NPC475096
0.5469 Remote Similarity NPC479450
0.5455 Remote Similarity NPC200092
0.5441 Remote Similarity NPC147596
0.5439 Remote Similarity NPC40377
0.5439 Remote Similarity NPC310661
0.5424 Remote Similarity NPC164599
0.541 Remote Similarity NPC302378
0.541 Remote Similarity NPC97326
0.5397 Remote Similarity NPC486107
0.5385 Remote Similarity NPC178851
0.5385 Remote Similarity NPC142319
0.5357 Remote Similarity NPC221090
0.5357 Remote Similarity NPC80098
0.5357 Remote Similarity NPC145900
0.5323 Remote Similarity NPC199335
0.5323 Remote Similarity NPC477240
0.5312 Remote Similarity NPC164857
0.5312 Remote Similarity NPC216752
0.5312 Remote Similarity NPC604892
0.5303 Remote Similarity NPC30432
0.5303 Remote Similarity NPC605700
0.5294 Remote Similarity NPC51328
0.5294 Remote Similarity NPC55158
0.5273 Remote Similarity NPC190730
0.527 Remote Similarity NPC215060
0.5254 Remote Similarity NPC606892
0.5246 Remote Similarity NPC104167
0.5238 Remote Similarity NPC276753
0.5238 Remote Similarity NPC190217
0.5238 Remote Similarity NPC205796
0.5238 Remote Similarity NPC611586
0.5231 Remote Similarity NPC210192
0.5211 Remote Similarity NPC476203
0.5211 Remote Similarity NPC473202
0.5179 Remote Similarity NPC12308
0.5161 Remote Similarity NPC34456
0.5161 Remote Similarity NPC604162
0.5156 Remote Similarity NPC37468
0.5156 Remote Similarity NPC246947
0.5156 Remote Similarity NPC604095
0.5156 Remote Similarity NPC610808
0.5152 Remote Similarity NPC177742
0.5152 Remote Similarity NPC99233
0.5152 Remote Similarity NPC485147
0.5147 Remote Similarity NPC76128
0.5147 Remote Similarity NPC606202
0.5143 Remote Similarity NPC199539
0.5091 Remote Similarity NPC9248
0.5082 Remote Similarity NPC105827
0.5079 Remote Similarity NPC475628
0.5075 Remote Similarity NPC486104
0.5075 Remote Similarity NPC486102
0.5075 Remote Similarity NPC606849

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC66968 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
0.5741 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