Structure

Physi-Chem Properties

Molecular Weight:  193.16
Volume:  215.337
LogP:  1.394
LogD:  0.341
LogS:  -1.884
# Rotatable Bonds:  2
TPSA:  50.41
# H-Bond Aceptor:  3
# H-Bond Donor:  3
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.654
Synthetic Accessibility Score:  4.366
Fsp3:  0.545
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:  -4.499
MDCK Permeability:  3.344421929796226e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.968
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.001
30% Bioavailability (F30%):  0.001

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.61
Plasma Protein Binding (PPB):  34.87959671020508%
Volume Distribution (VD):  1.502
Pgp-substrate:  75.75447082519531%

ADMET: Metabolism

CYP1A2-inhibitor:  0.022
CYP1A2-substrate:  0.675
CYP2C19-inhibitor:  0.032
CYP2C19-substrate:  0.91
CYP2C9-inhibitor:  0.006
CYP2C9-substrate:  0.354
CYP2D6-inhibitor:  0.578
CYP2D6-substrate:  0.897
CYP3A4-inhibitor:  0.015
CYP3A4-substrate:  0.514

ADMET: Excretion

Clearance (CL):  7.808
Half-life (T1/2):  0.574

ADMET: Toxicity

hERG Blockers:  0.084
Human Hepatotoxicity (H-HT):  0.184
Drug-inuced Liver Injury (DILI):  0.055
AMES Toxicity:  0.209
Rat Oral Acute Toxicity:  0.971
Maximum Recommended Daily Dose:  0.487
Skin Sensitization:  0.496
Carcinogencity:  0.172
Eye Corrosion:  0.003
Eye Irritation:  0.021
Respiratory Toxicity:  0.954

Download Data

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

  Natural Product: NPC325268

Natural Product ID:  NPC325268
Common Name*:   Nitensidine E
IUPAC Name:   6-methyl-6-[(1E)-4-methylpenta-1,3-dienyl]-4,5-dihydro-1H-pyrimidin-2-amine
Synonyms:   Nitensidine E
Standard InCHIKey:  HESWCJDXWDNXCR-GQCTYLIASA-N
Standard InCHI:  InChI=1S/C11H19N3/c1-9(2)5-4-6-11(3)7-8-13-10(12)14-11/h4-6H,7-8H2,1-3H3,(H3,12,13,14)/b6-4+
SMILES:  CC(=CC=CC1(CCN=C(N1)N)C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL561705
PubChem CID:   45267913
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001346] Diazines
        • [CHEMONTID:0000075] Pyrimidines and pyrimidine derivatives
          • [CHEMONTID:0002202] Hydropyrimidines

*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
NPO10824 Pterogyne nitens Species Fabaceae Eukaryota n.a. n.a. n.a. PMID[19159272]
NPO10824 Pterogyne nitens Species Fabaceae Eukaryota n.a. leaf n.a. PMID[19159272]
NPO10824 Pterogyne nitens Species Fabaceae 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
NPT116 Cell Line HL-60 Homo sapiens IC50 = 3.6 ug.mL-1 PMID[483714]
NPT180 Cell Line HCT-8 Homo sapiens IC50 > 5.0 ug.mL-1 PMID[483714]
NPT400 Cell Line MDA-MB-435 Homo sapiens IC50 > 5.0 ug.mL-1 PMID[483714]
NPT399 Cell Line SF-295 Homo sapiens IC50 = 4.9 ug.mL-1 PMID[483714]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 32.0 ug.mL-1 PMID[483715]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 16.0 ug.mL-1 PMID[483715]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 8.0 ug.mL-1 PMID[483715]

☑ 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 NPC325268 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
0.7667 Intermediate Similarity NPC153280
0.7333 Intermediate Similarity NPC32934
0.7119 Intermediate Similarity NPC188989
0.6707 Remote Similarity NPC471867
0.661 Remote Similarity NPC253366
0.661 Remote Similarity NPC97568
0.6296 Remote Similarity NPC57599
0.623 Remote Similarity NPC223653
0.6119 Remote Similarity NPC39250
0.5696 Remote Similarity NPC93070

  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 NPC325268 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
0.6393 Remote Similarity NPD9674 Approved
0.6393 Remote Similarity NPD9675 Approved
0.5795 Remote Similarity NPD305 Approved
0.5795 Remote Similarity NPD304 Approved
0.5733 Remote Similarity NPD1097 Approved
0.5733 Remote Similarity NPD1098 Approved
0.5714 Remote Similarity NPD543 Clinical (unspecified phase)
0.5604 Remote Similarity NPD9 Approved
0.5604 Remote Similarity NPD297 Approved

  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