Structure

Physi-Chem Properties

Molecular Weight:  600.42
Volume:  677.603
LogP:  4.627
LogD:  3.569
LogS:  -4.499
# Rotatable Bonds:  10
TPSA:  65.52
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  4
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.194
Synthetic Accessibility Score:  5.425
Fsp3:  0.55
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.294
MDCK Permeability:  1.5072175301611423e-05
Pgp-inhibitor:  0.505
Pgp-substrate:  0.043
Human Intestinal Absorption (HIA):  0.042
20% Bioavailability (F20%):  0.011
30% Bioavailability (F30%):  0.013

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.957
Plasma Protein Binding (PPB):  100.26419830322266%
Volume Distribution (VD):  1.059
Pgp-substrate:  6.306670665740967%

ADMET: Metabolism

CYP1A2-inhibitor:  0.079
CYP1A2-substrate:  0.912
CYP2C19-inhibitor:  0.968
CYP2C19-substrate:  0.932
CYP2C9-inhibitor:  0.836
CYP2C9-substrate:  0.984
CYP2D6-inhibitor:  0.915
CYP2D6-substrate:  0.945
CYP3A4-inhibitor:  0.983
CYP3A4-substrate:  0.929

ADMET: Excretion

Clearance (CL):  4.424
Half-life (T1/2):  0.071

ADMET: Toxicity

hERG Blockers:  0.596
Human Hepatotoxicity (H-HT):  0.774
Drug-inuced Liver Injury (DILI):  0.029
AMES Toxicity:  0.18
Rat Oral Acute Toxicity:  0.077
Maximum Recommended Daily Dose:  0.974
Skin Sensitization:  0.532
Carcinogencity:  0.958
Eye Corrosion:  0.003
Eye Irritation:  0.161
Respiratory Toxicity:  0.953

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  Natural Product: NPC10559

Natural Product ID:  NPC10559
Common Name*:   violaxanthin
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  SZCBXWMUOPQSOX-WVJDLNGLSA-N
Standard InCHI:  InChI=1S/C40H56O4/c1-29(17-13-19-31(3)21-23-39-35(5,6)25-33(41)27-37(39,9)43-39)15-11-12-16-30(2)18-14-20-32(4)22-24-40-36(7,8)26-34(42)28-38(40,10)44-40/h11-24,33-34,41-42H,25-28H2,1-10H3/b12-11+,17-13+,18-14+,23-21+,24-22+,29-15+,30-16+,31-19+,32-20+/t33-,34-,37+,38+,39-,40-/m0/s1
SMILES:  C/C(=CC=CC=C(C=CC=C(C=C[C@@]12O[C@@]1(C[C@H](CC2(C)C)O)C)/C)/C)/C=C/C=C(/C=C/[C@@]34O[C@@]3(C[C@H](CC4(C)C)O)C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   448438
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001554] Tetraterpenoids
          • [CHEMONTID:0001277] Carotenoids
            • [CHEMONTID:0001410] Xanthophylls

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Seeds n.a. DOI[10.1002/(SICI)1097-0010(199909)79:12<1620::AID-JSFA410>3.0.CO;2-G]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. DOI[10.1007/s00217-002-0656-1]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. DOI[10.1007/s00217-015-2561-4]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota n.a. n.a. DOI[10.1016/j.foodchem.2007.07.014]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota n.a. n.a. DOI[10.1016/j.foodchem.2010.05.061]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. DOI[10.1016/j.foodchem.2010.05.061]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. DOI[10.1016/j.indcrop.2013.08.051]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota n.a. n.a. DOI[10.1016/j.ssnmr.2006.05.001]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. DOI[10.1016/j.yclnex.2017.01.002; 10.31989/ffhd.v6i3.245]DOI[10.1016/j.yclnex.2017.01.002; 10.31989/ffhd.v6i3.245]
NPO2300 Actinidia deliciosa Species Actinidiaceae Eukaryota Fruits Spanish DOI[10.1021/jf00010a019]
NPO2300 Actinidia deliciosa Species Actinidiaceae Eukaryota Fruits n.a. DOI[10.1021/jf00016a013]
NPO2300 Actinidia deliciosa Species Actinidiaceae Eukaryota n.a. Germany DOI[10.1021/jf00016a013]
NPO2300 Actinidia deliciosa Species Actinidiaceae Eukaryota n.a. Italy DOI[10.1021/jf00016a013]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. DOI[10.1080/09064710.2011.598543]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. DOI[10.1111/j.1365-2621.1989.tb04709.x]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. DOI[10.1111/j.1745-4530.2009.00507.x]
NPO2300 Actinidia deliciosa Species Actinidiaceae Eukaryota Fruits Turkey DOI[10.1111/j.1745-4557.2003.tb00250.x]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. DOI[10.15835/NBHA4017181]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. DOI[10.17221/540/2012-CJFS]
NPO2300 Actinidia deliciosa Species Actinidiaceae Eukaryota Fruits n.a. DOI[10.17660/ActaHortic.2003.610.16]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. DOI[10.2137/145960607781635822]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. DOI[10.2478/aoas-2014-0072]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. DOI[10.3136/NSKKK.48.606]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. DOI[10.3390/agriculture2030244]
NPO2300 Actinidia deliciosa Species Actinidiaceae Eukaryota Fruits n.a. PMID[10794642]
NPO2300 Actinidia deliciosa Species Actinidiaceae Eukaryota Fruits n.a. PMID[10820090]
NPO2300 Actinidia deliciosa Species Actinidiaceae Eukaryota Fruits n.a. PMID[11754554]
NPO2300 Actinidia deliciosa Species Actinidiaceae Eukaryota Fruits n.a. PMID[15315387]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. PMID[15563205]
NPO2300 Actinidia deliciosa Species Actinidiaceae Eukaryota Fruits n.a. PMID[16076125]
NPO2300 Actinidia deliciosa Species Actinidiaceae Eukaryota Fruits n.a. PMID[16920856]
NPO2300 Actinidia deliciosa Species Actinidiaceae Eukaryota Fruits n.a. PMID[19358604]
NPO2300 Actinidia deliciosa Species Actinidiaceae Eukaryota Fruits n.a. PMID[21190690]
NPO2300 Actinidia deliciosa Species Actinidiaceae Eukaryota Fruits n.a. PMID[23394984]
NPO2300 Actinidia deliciosa Species Actinidiaceae Eukaryota n.a. Germany PMID[23394984]
NPO2300 Actinidia deliciosa Species Actinidiaceae Eukaryota n.a. New Zealand PMID[23394984]
NPO2300 Actinidia deliciosa Species Actinidiaceae Eukaryota Fruits n.a. PMID[2413754]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. PMID[25026919]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. PMID[25977015]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. PMID[26351516]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. PMID[27556441]
NPO41864 A new engineered strain of Escherichia coli BL21(DE3) [laad pdc adh gdh] Strain Enterobacteriaceae Bacteria n.a. n.a. n.a. PMID[29560727]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits Schirgiswalde, Germany 2008-Aug PMID[31206724]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits Cracow, Poland 2008-Sep PMID[31206724]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits Schirgiswalde, Germany 2008-Sep PMID[31206724]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits Schirgiswalde, Germany 2008-Oct PMID[31206724]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. PMID[31619015]
NPO5973 Sonchus asper Species Asteraceae Eukaryota n.a. Molise Region, Italy Autumn 2018 PMID[32803719]
NPO5973 Sonchus asper Species Asteraceae Eukaryota n.a. Molise Region, Italy Spring 2019 PMID[32803719]
NPO5973 Sonchus asper Species Asteraceae Eukaryota n.a. Molise Region, Italy PMID[32803719]
NPO7252 Sonchus oleraceus Species Asteraceae Eukaryota n.a. Molise Region, Italy Autumn 2018 PMID[32803719]
NPO7252 Sonchus oleraceus Species Asteraceae Eukaryota n.a. Molise Region, Italy Spring 2019 PMID[32803719]
NPO7252 Sonchus oleraceus Species Asteraceae Eukaryota n.a. Molise Region, Italy PMID[32803719]
NPO5973 Sonchus asper Species Asteraceae Eukaryota n.a The rural area of Viçosa, State of Minas Gerais (MG), Brazil Adult stage PMID[35282307]
NPO7252 Sonchus oleraceus Species Asteraceae Eukaryota n.a The rural area of Viçosa, State of Minas Gerais (MG), Brazil Adult stage PMID[35282307]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Flowers n.a. PMID[9301422]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. PMID[9301422]
NPO2300 Actinidia deliciosa Species Actinidiaceae Eukaryota Fruits n.a. PMID[9542132]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota n.a. n.a. Database[FooDB]
NPO7269 Aronia melanocarpa Species Rosaceae Eukaryota Fruits n.a. Database[Phenol-Explorer]
NPO5973 Sonchus asper Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2300 Actinidia deliciosa Species Actinidiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2300 Actinidia deliciosa Species Actinidiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7252 Sonchus oleraceus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5973 Sonchus asper Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7269 Aronia melanocarpa Species Rosaceae 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 NP ID Organism Material Preparation Organism Part NP Quantity (Standard) NP Quantity (Minimum) NP Quantity (Maximum) Quantity Unit Reference
NPO2300 NPC10559 n.a. Fruits 0.093 n.a. n.a. mg/100g of FW DOI[10.1021/jf00010a019]
NPO11328.1 NPC10559 n.a. Fruits 0.19 n.a. n.a. mg/100g of FW PMID[11754554]
NPO2300 NPC10559 n.a. Fruits 0.09 n.a. n.a. mg/100g of FW PMID[11754554]
NPO7269 NPC10559 n.a. Fruits 4.5 n.a. n.a. mg/kg DOI[10.1111/j.1365-2621.1989.tb04709.x]
NPO14569 NPC10559 n.a. n.a. 1.4 n.a. n.a. mg/100g WB PMID[32803719]
NPO14569 NPC10559 n.a. n.a. 1.1 n.a. n.a. mg/100g WB PMID[32803719]
NPO14569 NPC10559 n.a. n.a. 1.3 n.a. n.a. mg/100g WB PMID[32803719]
NPO5973 NPC10559 n.a. n.a. 3.4 n.a. n.a. mg/100g WB PMID[32803719]
NPO5973 NPC10559 n.a. n.a. 4.4 n.a. n.a. mg/100g WB PMID[32803719]
NPO5973 NPC10559 n.a. n.a. 3.9 n.a. n.a. mg/100g WB PMID[32803719]
NPO7252 NPC10559 n.a. n.a. 3.9 n.a. n.a. mg/100g WB PMID[32803719]
NPO7252 NPC10559 n.a. n.a. 3.1 n.a. n.a. mg/100g WB PMID[32803719]

☑ 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

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

  Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

●  The left chart: Distribution of similarity level between NPC10559 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID

  Chemically structural similarity: II. Similar Clinical/Approved Drugs

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

●  The left chart: Distribution of similarity level between NPC10559 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage

  Bioactivity similarity: Similar Natural Products in NPASS

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