Structure

Physi-Chem Properties

Molecular Weight:  198.08
Volume:  205.404
LogP:  1.533
LogD:  1.452
LogS:  -3.21
# Rotatable Bonds:  0
TPSA:  48.65
# H-Bond Aceptor:  3
# H-Bond Donor:  2
# Rings:  3
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.572
Synthetic Accessibility Score:  2.784
Fsp3:  0.083
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.948
MDCK Permeability:  7.245324468385661e-06
Pgp-inhibitor:  0.001
Pgp-substrate:  0.726
Human Intestinal Absorption (HIA):  0.013
20% Bioavailability (F20%):  0.687
30% Bioavailability (F30%):  0.24

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.787
Plasma Protein Binding (PPB):  74.28522491455078%
Volume Distribution (VD):  1.0
Pgp-substrate:  17.941516876220703%

ADMET: Metabolism

CYP1A2-inhibitor:  0.987
CYP1A2-substrate:  0.947
CYP2C19-inhibitor:  0.698
CYP2C19-substrate:  0.083
CYP2C9-inhibitor:  0.233
CYP2C9-substrate:  0.783
CYP2D6-inhibitor:  0.786
CYP2D6-substrate:  0.865
CYP3A4-inhibitor:  0.522
CYP3A4-substrate:  0.215

ADMET: Excretion

Clearance (CL):  5.826
Half-life (T1/2):  0.622

ADMET: Toxicity

hERG Blockers:  0.025
Human Hepatotoxicity (H-HT):  0.734
Drug-inuced Liver Injury (DILI):  0.931
AMES Toxicity:  0.824
Rat Oral Acute Toxicity:  0.948
Maximum Recommended Daily Dose:  0.902
Skin Sensitization:  0.903
Carcinogencity:  0.49
Eye Corrosion:  0.037
Eye Irritation:  0.966
Respiratory Toxicity:  0.982

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

  Natural Product: NPC175899

Natural Product ID:  NPC175899
Common Name*:   SATMZMMKDDTOSQ-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  SATMZMMKDDTOSQ-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C12H10N2O/c1-7-12-10(4-5-13-7)9-3-2-8(15)6-11(9)14-12/h2-6,14-15H,1H3
SMILES:  Cc1c2c(ccn1)c1ccc(cc1[nH]2)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   n.a.
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000279] Alkaloids and derivatives
      • [CHEMONTID:0001140] Harmala alkaloids

*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
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. fruit n.a. PMID[16417304]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. branch n.a. PMID[17202693]
NPO1085 Peganum harmala Species Nitrariaceae Eukaryota Seeds n.a. n.a. PMID[28128938]
NPO1085 Peganum harmala Species Nitrariaceae Eukaryota n.a. n.a. n.a. PMID[6736972]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota Bark n.a. n.a. Database[FooDB]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. n.a. Database[FooDB]
NPO1085 Peganum harmala Species Nitrariaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3808 Elaeagnus angustifolia Species Elaeagnaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO3808 Elaeagnus angustifolia Species Elaeagnaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1085 Peganum harmala Species Nitrariaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1085 Peganum harmala Species Nitrariaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO3808 Elaeagnus angustifolia Species Elaeagnaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2926 Phallus rugulosus Species Phallaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1085 Peganum harmala Species Nitrariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5736 Banisteriopsis inebrians Species Malpighiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15095 Hippophae rhamnoides Species Elaeagnaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3808 Elaeagnus angustifolia Species Elaeagnaceae 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
NPT3114 Individual Protein Dual-specificity tyrosine-phosphorylation regulated kinase 1A Homo sapiens IC50 = 90.0 nM PMID[519905]
NPT173 Organism Klebsiella pneumoniae Klebsiella pneumoniae Inhibition = 20.45 % PMID[519906]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa Inhibition = 15.56 % PMID[519906]
NPT20 Organism Candida albicans Candida albicans Inhibition = 2.57 % PMID[519906]
NPT85 Organism Filobasidiella neoformans Cryptococcus neoformans Inhibition = -8.88 % PMID[519906]
NPT747 Organism Acinetobacter baumannii Acinetobacter baumannii Inhibition = -8.06 % PMID[519906]
NPT19 Organism Escherichia coli Escherichia coli Inhibition = 7.41 % PMID[519906]
NPT2922 Organism Staphylococcus aureus subsp. aureus Staphylococcus aureus subsp. aureus Inhibition = 18.39 % PMID[519906]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 IC50 > 20000.0 nM PMID[519907]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 IC50 > 19952.62 nM PMID[519907]

☑ 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 NPC175899 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 NPC175899 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