Structure

Physi-Chem Properties

Molecular Weight:  110.06
Volume:  105.262
LogP:  -2.977
LogD:  -1.483
LogS:  -1.444
# Rotatable Bonds:  0
TPSA:  79.28
# H-Bond Aceptor:  4
# H-Bond Donor:  4
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.341
Synthetic Accessibility Score:  4.43
Fsp3:  0.0
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:  -5.246
MDCK Permeability:  0.0015027641784399748
Pgp-inhibitor:  0.0
Pgp-substrate:  0.733
Human Intestinal Absorption (HIA):  0.191
20% Bioavailability (F20%):  0.094
30% Bioavailability (F30%):  0.012

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.745
Plasma Protein Binding (PPB):  12.007421493530273%
Volume Distribution (VD):  0.827
Pgp-substrate:  74.9583740234375%

ADMET: Metabolism

CYP1A2-inhibitor:  0.012
CYP1A2-substrate:  0.382
CYP2C19-inhibitor:  0.104
CYP2C19-substrate:  0.035
CYP2C9-inhibitor:  0.009
CYP2C9-substrate:  0.011
CYP2D6-inhibitor:  0.006
CYP2D6-substrate:  0.167
CYP3A4-inhibitor:  0.002
CYP3A4-substrate:  0.123

ADMET: Excretion

Clearance (CL):  2.155
Half-life (T1/2):  0.889

ADMET: Toxicity

hERG Blockers:  0.071
Human Hepatotoxicity (H-HT):  0.992
Drug-inuced Liver Injury (DILI):  0.924
AMES Toxicity:  0.63
Rat Oral Acute Toxicity:  0.67
Maximum Recommended Daily Dose:  0.489
Skin Sensitization:  0.851
Carcinogencity:  0.955
Eye Corrosion:  0.007
Eye Irritation:  0.789
Respiratory Toxicity:  0.932

Download Data

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

  Natural Product: NPC230087

Natural Product ID:  NPC230087
Common Name*:   Diaminopyrimidine
IUPAC Name:   pyrimidine-2,4-diamine
Synonyms:   Diaminopyrimidine
Standard InCHIKey:  YAAWASYJIRZXSZ-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C4H6N4/c5-3-1-2-7-4(6)8-3/h1-2H,(H4,5,6,7,8)
SMILES:  N=c1cc[nH]c(=N)[nH]1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1233987
PubChem CID:   67431
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001346] Diazines
        • [CHEMONTID:0000075] Pyrimidines and pyrimidine derivatives
          • [CHEMONTID:0001262] Aminopyrimidines and derivatives

*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
NPO18950 Cephalotaxus fortunei Species Taxaceae Eukaryota n.a. n.a. n.a. PMID[12542368]
NPO18950 Cephalotaxus fortunei Species Taxaceae Eukaryota n.a. n.a. n.a. PMID[28139925]
NPO18950 Cephalotaxus fortunei Species Taxaceae Eukaryota n.a. n.a. n.a. PMID[31184894]
NPO18950 Cephalotaxus fortunei Species Taxaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18950 Cephalotaxus fortunei Species Taxaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18950 Cephalotaxus fortunei Species Taxaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18950 Cephalotaxus fortunei Species Taxaceae 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
NPT2818 Individual Protein Dihydrofolate reductase Homo sapiens Ki = 180000.0 nM PMID[520792]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 2.0 ug.mL-1 PMID[520791]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 0.5 ug.mL-1 PMID[520791]
NPT2 Others Unspecified Ratio Ki = 10.0 n.a. PMID[520792]
NPT2 Others Unspecified Ki = 1800000.0 nM PMID[520792]

☑ 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 NPC230087 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
0.7547 Intermediate Similarity NPC212436
0.6964 Remote Similarity NPC39250
0.68 Remote Similarity NPC57565
0.6346 Remote Similarity NPC253366
0.6346 Remote Similarity NPC97568
0.6296 Remote Similarity NPC188989
0.625 Remote Similarity NPC32934
0.6122 Remote Similarity NPC31657
0.5918 Remote Similarity NPC163099

  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 NPC230087 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
0.68 Remote Similarity NPD8841 Approved
0.6667 Remote Similarity NPD1097 Approved
0.6667 Remote Similarity NPD8844 Approved
0.6667 Remote Similarity NPD1098 Approved
0.6667 Remote Similarity NPD8843 Phase 3
0.6562 Remote Similarity NPD9643 Approved
0.6471 Remote Similarity NPD1144 Phase 2
0.6364 Remote Similarity NPD8570 Approved
0.6275 Remote Similarity NPD9015 Phase 2
0.619 Remote Similarity NPD9642 Approved
0.6 Remote Similarity NPD9059 Approved
0.5823 Remote Similarity NPD1353 Suspended

  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