Structure

Physi-Chem Properties

Molecular Weight:  195.08
Volume:  174.534
LogP:  -1.474
LogD:  -0.555
LogS:  -2.672
# Rotatable Bonds:  1
TPSA:  99.55
# H-Bond Aceptor:  7
# H-Bond Donor:  3
# Rings:  2
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.548
Synthetic Accessibility Score:  3.628
Fsp3:  0.286
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:  -5.695
MDCK Permeability:  6.7357555963099e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.808
Human Intestinal Absorption (HIA):  0.818
20% Bioavailability (F20%):  0.023
30% Bioavailability (F30%):  0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.648
Plasma Protein Binding (PPB):  53.274192810058594%
Volume Distribution (VD):  1.079
Pgp-substrate:  37.41199493408203%

ADMET: Metabolism

CYP1A2-inhibitor:  0.02
CYP1A2-substrate:  0.965
CYP2C19-inhibitor:  0.033
CYP2C19-substrate:  0.045
CYP2C9-inhibitor:  0.005
CYP2C9-substrate:  0.007
CYP2D6-inhibitor:  0.005
CYP2D6-substrate:  0.101
CYP3A4-inhibitor:  0.006
CYP3A4-substrate:  0.269

ADMET: Excretion

Clearance (CL):  7.283
Half-life (T1/2):  0.876

ADMET: Toxicity

hERG Blockers:  0.024
Human Hepatotoxicity (H-HT):  0.989
Drug-inuced Liver Injury (DILI):  0.976
AMES Toxicity:  0.028
Rat Oral Acute Toxicity:  0.585
Maximum Recommended Daily Dose:  0.031
Skin Sensitization:  0.117
Carcinogencity:  0.895
Eye Corrosion:  0.003
Eye Irritation:  0.023
Respiratory Toxicity:  0.936

Download Data

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

  Natural Product: NPC17940

Natural Product ID:  NPC17940
Common Name*:   DAHAOEBKKGDLMP-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  DAHAOEBKKGDLMP-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C7H9N5O2/c1-12-3-4(10-7(12)13)9-6(8)11-5(3)14-2/h1-2H3,(H3,8,9,10,11,13)
SMILES:  Cn1c2c([nH]c(=N)nc2OC)nc1O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   10584006
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001797] Imidazopyrimidines
        • [CHEMONTID:0000245] Purines and purine derivatives
          • [CHEMONTID:0000597] Purinones
            • [CHEMONTID:0000246] Hypoxanthines

*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
NPO362 Gentiana crassicaulis Species Gentianaceae Eukaryota n.a. n.a. n.a. PMID[33052051]
NPO362 Gentiana crassicaulis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7985 Swertia tosaensis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1442 Viburnum dilatatum Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7985 Swertia tosaensis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO362 Gentiana crassicaulis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3490 Aragoa cundinamarcensis Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO362 Gentiana crassicaulis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO362 Gentiana crassicaulis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO362 Gentiana crassicaulis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8729 Symplegma rubra Species Styelidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5407 Polypodium pedatum Species Polypodiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5046 Lisianthus chelonoides n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO3490 Aragoa cundinamarcensis Species Plantaginaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5242 Sideritis argyrea Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1442 Viburnum dilatatum Species Adoxaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7985 Swertia tosaensis Species Gentianaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6384 Euryops spathaceus Species Asteraceae 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

☑ 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 NPC17940 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 NPC17940 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