Natural Product: NPC186902

Natural Product IDNPC186902
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
 PHYYADMVYQURSX-WWFIZPDBSA-N
IUPAC Name n.a.
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier n.a.
PubChem CID 9548622
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
              • [CHEMONTID:0000373] Glucosinolates
                • [CHEMONTID:0003925] Alkylglucosinolates

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 PHYYADMVYQURSX-WWFIZPDBSA-N
Standard InCHI InChI=1S/C11H21NO10S3/c1-24(17)4-2-3-7(12-22-25(18,19)20)23-11-10(16)9(15)8(14)6(5-13)21-11/h6,8-11,13-16H,2-5H2,1H3,(H,18,19,20)/b12-7+/t6-,8-,9+,10-,11+,24?/m1/s1
SMILES CS(=O)CCC/C(=NOS(=O)(=O)O)/S[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   423.03 Volume:   342.045
?
Van der Waals volume.
Dense:   1.237 LogP:   -2.185
?
The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   -0.662
?
The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
 LogS:   -1.505
?
The logarithm of aqueous solubility value.
Rotatable Bonds:   9.0 Rigid Bonds:   9.0
TPSA:   189.17
?
Topological Polar Surface Area.
 H-Bond Acceptor:   11.0
H-Bond Donor:   5.0 Rings:   1.0
Heavy Atoms:   14.0

MedChem Properties

QED Drug-Likeness Score:   0.094 GASA:   0.0
?
GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   5.161 Fsp3:   0.909
MCE-18:   32.19
?
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:   Accepted
Golden Triangle Rule:   Rejected BMS Rule:   0
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.16 Fluc inhibitor:   0.0
?
The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.01
?
The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
 Green fluorescence:   0.066
?
The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.774 Promiscuous compounds:   0.052

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -5.906 MDCK Permeability:   -5.019
Pgp-inhibitor:   0.0 Pgp-substrate:   0.0
PAMPA:   0.993
?
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):   0.933
20% Bioavailability (F20%):   0.217 30% Bioavailability (F30%):   0.997
50% Bioavailability (F50%):   0.888

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.036 MRP1:   0.079
Plasma Protein Binding (PPB):   35.145% Volume Distribution (VD):   -0.591
Fu: 64.189%
?
The fraction unbound in plasms.
 OATP1B1 inhibitor:   0.986
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.0
BSEP inhibitor:   0.003

ADMET: Metabolism

CYP1A2-inhibitor:   0.0 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.0
CYP2C9-inhibitor:   0.057 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:   0.0
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):  1.253 Half-life (T1/2):  1.908

ADMET: Toxicity

hERG Blockers:  0.0 hERG Blockers (10um):  0.012
Human Hepatotoxicity (H-HT):  0.402 Drug-induced Liver Injury (DILI):  0.797
AMES Toxicity:  0.894 Rat Oral Acute Toxicity:  0.211
Maximum Recommended Daily Dose:  0.577 Skin Sensitization:  1.0
Carcinogencity:  0.263 Eye Corrosion:  0.002
Eye Irritation:  0.356 Respiratory Toxicity:  0.205
Drug-induced Neurotoxicity:  0.0 Ototoxicity:  0.238
Hematotoxicity:  0.069 Drug-induced Nephrotoxicity:  0.09
Genotoxicity:  1.0 RPMI-8226 Immunitoxicity:  0.025
A549 Cytotoxicity:  0.0 Hek293 Cytotoxicity:  0.35
BCF:   0.3
?
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:   2.828
?
48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.202
?
48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
 LC50FM:   3.599
?
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
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jfca.2004.07.004]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.jfca.2005.08.001]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. retail stores, supermarkets and market stalls in Forssa and in the Helsinki area 2003–2005 DOI[10.1016/j.jfca.2006.05.007]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. 1996-Sep PMID[10352947]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. PMID[15877880]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota Fruits n.a. n.a. PMID[16309325]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. Seoul, Korea 2000-Jun PMID[16643034]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. PMID[17011103]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. PMID[18460139]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. Northeastern Regional Plant Introduction Station at Geneva 1966, 1967, and 1968 crop seasons PMID[18460139]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota fruit n.a. n.a. PMID[18505286]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota fruit n.a. n.a. PMID[19650637]
NPO2978 Croton tiglium Species Euphorbiaceae Eukaryota n.a. seed n.a. PMID[21049973]
NPO13645 Armoracia rusticana Species Brassicaceae Eukaryota n.a. root n.a. PMID[22779710]
NPO13645 Armoracia rusticana Species Brassicaceae Eukaryota n.a. n.a. n.a. PMID[22779710]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota fruits n.a. n.a. PMID[23305920]
NPO2978 Croton tiglium Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[23701597]
NPO2978 Croton tiglium Species Euphorbiaceae Eukaryota n.a. n.a. n.a. PMID[25819096]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. PMID[2831703]
NPO13645 Armoracia rusticana Species Brassicaceae Eukaryota Roots n.a. n.a. PMID[31625742]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. PMID[32141747]
NPO30934 Armoracia lapathifolia Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13645 Armoracia rusticana Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO16511 Iberis amara Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO2978 Croton tiglium Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO13645 Armoracia rusticana Species Brassicaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota Roots n.a. Database[FooDB]
NPO13645 Armoracia rusticana Species Brassicaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO13645 Armoracia rusticana Species Brassicaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO13645 Armoracia rusticana Species Brassicaceae Eukaryota n.a. n.a. Database[FooDB]
NPO16511 Iberis amara Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO30934 Armoracia lapathifolia Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2978 Croton tiglium Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO13645 Armoracia rusticana Species Brassicaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13645 Armoracia rusticana Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16511 Iberis amara Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2978 Croton tiglium Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2978 Croton tiglium Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7576.2 Brassica oleracea var. sabauda Varieties Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO30934 Armoracia lapathifolia Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16511 Iberis amara Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO2978 Croton tiglium Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9518 Gardenia jasminoides Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2978 Croton tiglium Species Euphorbiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16511 Iberis amara Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13645 Armoracia rusticana Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9518 Gardenia jasminoides Species Rubiaceae 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
NPO7576.2 Brassica oleracea var. sabauda n.a. n.a. 1.5 n.a. n.a. µmol/100g of FW PMID[17011103]
NPO7576.2 Brassica oleracea var. sabauda n.a. n.a. 17.1 n.a. n.a. µmol/100g of FW PMID[17011103]
NPO7576.2 Brassica oleracea var. sabauda n.a. n.a. 3.88 n.a. n.a. µmol/100g of FW PMID[17011103]

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 NPC186902 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
0.6481 Remote Similarity NPC320012

Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC186902 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