Structure

Physi-Chem Properties

Molecular Weight:  354.1
Volume:  325.553
LogP:  -0.322
LogD:  -0.392
LogS:  -2.018
# Rotatable Bonds:  2
TPSA:  160.82
# H-Bond Aceptor:  9
# H-Bond Donor:  6
# Rings:  3
# Heavy Atoms:  9

MedChem Properties

QED Drug-Likeness Score:  0.398
Synthetic Accessibility Score:  4.023
Fsp3:  0.438
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.105
MDCK Permeability:  1.0201457371294964e-05
Pgp-inhibitor:  0.004
Pgp-substrate:  0.994
Human Intestinal Absorption (HIA):  0.835
20% Bioavailability (F20%):  0.198
30% Bioavailability (F30%):  0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.055
Plasma Protein Binding (PPB):  74.76331329345703%
Volume Distribution (VD):  1.035
Pgp-substrate:  30.509817123413086%

ADMET: Metabolism

CYP1A2-inhibitor:  0.086
CYP1A2-substrate:  0.094
CYP2C19-inhibitor:  0.016
CYP2C19-substrate:  0.096
CYP2C9-inhibitor:  0.005
CYP2C9-substrate:  0.473
CYP2D6-inhibitor:  0.01
CYP2D6-substrate:  0.167
CYP3A4-inhibitor:  0.017
CYP3A4-substrate:  0.024

ADMET: Excretion

Clearance (CL):  3.384
Half-life (T1/2):  0.811

ADMET: Toxicity

hERG Blockers:  0.03
Human Hepatotoxicity (H-HT):  0.196
Drug-inuced Liver Injury (DILI):  0.965
AMES Toxicity:  0.742
Rat Oral Acute Toxicity:  0.049
Maximum Recommended Daily Dose:  0.011
Skin Sensitization:  0.409
Carcinogencity:  0.031
Eye Corrosion:  0.003
Eye Irritation:  0.071
Respiratory Toxicity:  0.131

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General Info & Identifiers & Properties  
Structure MOL file  
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Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC55597

Natural Product ID:  NPC55597
Common Name*:   UDTUCCXZNVRBEJ-PBVFJORSSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  UDTUCCXZNVRBEJ-PBVFJORSSA-N
Standard InCHI:  InChI=1S/C16H18O9/c1-5-2-6(18)10-7(19)3-8(20)11(15(10)24-5)16-14(23)13(22)12(21)9(4-17)25-16/h2-3,9,12-14,16-17,19-23H,4H2,1H3/t9-,12-,13+,14-,16+/m1/s1
SMILES:  Cc1cc(=O)c2c(cc(c(c2o1)[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   10338198
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

*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
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[1402962]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota Flower Buds n.a. n.a. PMID[26977531]
NPO8622 Stauntonia hexaphylla Species Lardizabalaceae Eukaryota Fruits n.a. n.a. PMID[31301930]
NPO6783 Avrainvillea rawsonii Species Udoteaceae Eukaryota n.a. n.a. n.a. PMID[7964790]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. PMID[8904847]
NPO8622 Stauntonia hexaphylla Species Lardizabalaceae Eukaryota n.a. n.a. n.a. Database[Article]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota Bark n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota Essential Oil n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. Database[FooDB]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. Database[FooDB]
NPO1032 Piper attenuatum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7626 Damnacanthus major Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8622 Stauntonia hexaphylla Species Lardizabalaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1934 Strychnos triplinervia Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO577 Lactifluus subvellereus Species Russulaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1032 Piper attenuatum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8622 Stauntonia hexaphylla Species Lardizabalaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7626 Damnacanthus major Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1934 Strychnos triplinervia Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2395 Siphonaria australis Species Siphonariidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO577 Lactifluus subvellereus Species Russulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1032 Piper attenuatum Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1934 Strychnos triplinervia Species Loganiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO173 Aconitum sajanense Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4504 Cassia jahnii Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3987 Syzygium aromaticum Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6072 Andinobates bombetes Species Dendrobatidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9718 Cyphelium chrysocephalum Species Caliciaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12409 Artemisia jacutica Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7626 Damnacanthus major Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5834 Pellicularia sasakii n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO8622 Stauntonia hexaphylla Species Lardizabalaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6041 Lithocolletis coryli n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO9456 Rubus sanctus Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6783 Avrainvillea rawsonii Species Udoteaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15735 Galeocerdo arcticus Species Carcharhinidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1456 Bersama abyssinica Species Melianthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7383 Puccinia lagenophorae Species Pucciniaceae 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

☑ 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
NPT113 Cell Line RAW264.7 Mus musculus IC50 = 46000.0 nM PMID[26977531]
NPT113 Cell Line RAW264.7 Mus musculus IC50 > 60000.0 nM PMID[26977531]

☑ 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 NPC55597 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 NPC55597 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