Structure

Physi-Chem Properties

Molecular Weight:  319.1
Volume:  312.735
LogP:  3.069
LogD:  2.667
LogS:  -4.603
# Rotatable Bonds:  0
TPSA:  91.14
# H-Bond Aceptor:  6
# H-Bond Donor:  3
# Rings:  5
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.434
Synthetic Accessibility Score:  2.66
Fsp3:  0.111
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.309
MDCK Permeability:  1.1144338714075275e-05
Pgp-inhibitor:  0.034
Pgp-substrate:  0.057
Human Intestinal Absorption (HIA):  0.02
20% Bioavailability (F20%):  0.161
30% Bioavailability (F30%):  0.797

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.08
Plasma Protein Binding (PPB):  96.35582733154297%
Volume Distribution (VD):  0.469
Pgp-substrate:  2.7979812622070312%

ADMET: Metabolism

CYP1A2-inhibitor:  0.978
CYP1A2-substrate:  0.215
CYP2C19-inhibitor:  0.396
CYP2C19-substrate:  0.062
CYP2C9-inhibitor:  0.651
CYP2C9-substrate:  0.794
CYP2D6-inhibitor:  0.692
CYP2D6-substrate:  0.838
CYP3A4-inhibitor:  0.384
CYP3A4-substrate:  0.228

ADMET: Excretion

Clearance (CL):  6.281
Half-life (T1/2):  0.743

ADMET: Toxicity

hERG Blockers:  0.014
Human Hepatotoxicity (H-HT):  0.615
Drug-inuced Liver Injury (DILI):  0.469
AMES Toxicity:  0.826
Rat Oral Acute Toxicity:  0.091
Maximum Recommended Daily Dose:  0.479
Skin Sensitization:  0.757
Carcinogencity:  0.881
Eye Corrosion:  0.003
Eye Irritation:  0.67
Respiratory Toxicity:  0.931

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

  Natural Product: NPC224900

Natural Product ID:  NPC224900
Common Name*:   PRSXYIFCRMRNRJ-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  PRSXYIFCRMRNRJ-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C18H13N3O3/c22-13-6-5-11-14(16(13)23)20-17-15-10(7-8-21(17)18(11)24)9-3-1-2-4-12(9)19-15/h1-6,19,22-23H,7-8H2
SMILES:  c1ccc2c(c1)c1CCn3c(-c1[nH]2)nc1c(ccc(c1O)O)c3=O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   23250595
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000211] Indoles and derivatives
        • [CHEMONTID:0001213] Pyridoindoles
          • [CHEMONTID:0001914] Beta carbolines

*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
NPO16519 Persea americana Species Lauraceae Eukaryota n.a. fruit n.a. PMID[10820058]
NPO22654 Millettia pachycarpa Species Fabaceae Eukaryota n.a. leaf n.a. PMID[16441086]
NPO16519 Persea americana Species Lauraceae Eukaryota Unripe fruit n.a. n.a. PMID[9644064]
NPO16519 Persea americana Species Lauraceae Eukaryota n.a. n.a. Database[FooDB]
NPO16519 Persea americana Species Lauraceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO16519 Persea americana Species Lauraceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO16519 Persea americana Species Lauraceae Eukaryota n.a. n.a. Database[FooDB]
NPO16519 Persea americana Species Lauraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO22654 Millettia pachycarpa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16519 Persea americana Species Lauraceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO16519 Persea americana Species Lauraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22654 Millettia pachycarpa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO22654 Millettia pachycarpa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16519 Persea americana Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3683.1 Pteridium aquilinum subsp. latiusculum Subspecies Dennstaedtiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20117 Leucas lanata Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4954 Eleutherococcus divaricatus Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22654 Millettia pachycarpa Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22779 Sphagnum magellanicum Species Sphagnaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23009 Udotea flabellum Species Udoteaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22962 Coussarea hydrangeifolia Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29067 Spondias dulcis Species Anacardiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10669 Cousinia pterocaulos Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22906 Bouchardatia neurococca Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22204 Tylostylis discolor n.a. n.a. n.a. 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

☑ 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 NPC224900 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 NPC224900 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