Structure

Physi-Chem Properties

Molecular Weight:  137.06
Volume:  129.091
LogP:  0.372
LogD:  0.506
LogS:  -0.807
# Rotatable Bonds:  0
TPSA:  46.92
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.547
Synthetic Accessibility Score:  3.208
Fsp3:  0.333
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:  -4.418
MDCK Permeability:  7.104927135515027e-06
Pgp-inhibitor:  0.0
Pgp-substrate:  0.189
Human Intestinal Absorption (HIA):  0.034
20% Bioavailability (F20%):  0.049
30% Bioavailability (F30%):  0.103

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.707
Plasma Protein Binding (PPB):  17.371950149536133%
Volume Distribution (VD):  0.961
Pgp-substrate:  73.67952728271484%

ADMET: Metabolism

CYP1A2-inhibitor:  0.243
CYP1A2-substrate:  0.747
CYP2C19-inhibitor:  0.14
CYP2C19-substrate:  0.227
CYP2C9-inhibitor:  0.039
CYP2C9-substrate:  0.538
CYP2D6-inhibitor:  0.058
CYP2D6-substrate:  0.26
CYP3A4-inhibitor:  0.118
CYP3A4-substrate:  0.335

ADMET: Excretion

Clearance (CL):  7.142
Half-life (T1/2):  0.838

ADMET: Toxicity

hERG Blockers:  0.031
Human Hepatotoxicity (H-HT):  0.237
Drug-inuced Liver Injury (DILI):  0.953
AMES Toxicity:  0.143
Rat Oral Acute Toxicity:  0.114
Maximum Recommended Daily Dose:  0.897
Skin Sensitization:  0.698
Carcinogencity:  0.295
Eye Corrosion:  0.003
Eye Irritation:  0.017
Respiratory Toxicity:  0.035

Download Data

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

  Natural Product: NPC273327

Natural Product ID:  NPC273327
Common Name*:   7,8-Dihydro-6H-Imidazo[1,5-C]Pyrimidin-5-One
IUPAC Name:   7,8-dihydro-6H-imidazo[1,5-c]pyrimidin-5-one
Synonyms:  
Standard InCHIKey:  AZFYLSFUALTNAY-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C6H7N3O/c10-6-8-2-1-5-3-7-4-9(5)6/h3-4H,1-2H2,(H,8,10)
SMILES:  C1CN=C(n2cncc12)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1780255
PubChem CID:   1487518
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001797] Imidazopyrimidines

*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
NPO11745 Subergorgia suberosa Species Subergorgiidae Eukaryota n.a. Taiwanese gorgonian coral n.a. PMID[12088433]
NPO11745 Subergorgia suberosa Species Subergorgiidae Eukaryota n.a. Taiwanese Gorgonian coral n.a. PMID[12141868]
NPO11745 Subergorgia suberosa Species Subergorgiidae Eukaryota n.a. n.a. n.a. PMID[16124781]
NPO11745 Subergorgia suberosa Species Subergorgiidae Eukaryota n.a. n.a. n.a. PMID[18290631]
NPO9032 Geotrichum candidum Species Dipodascaceae Eukaryota n.a. n.a. n.a. PMID[20488699]
NPO11870 Rhododendron arboreum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11870 Rhododendron arboreum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9032 Geotrichum candidum Species Dipodascaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11745 Subergorgia suberosa Species Subergorgiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11870 Rhododendron arboreum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12594 Hybanthus enneaspermus Species Violaceae 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
NPT2 Others Unspecified IC50 = 24200.0 nM PMID[537313]

☑ 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 NPC273327 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
0.87 High Similarity NPC326248
0.87 High Similarity NPC187191
0.819 Intermediate Similarity NPC155498
0.8173 Intermediate Similarity NPC111132
0.8165 Intermediate Similarity NPC327613
0.7833 Intermediate Similarity NPC470138
0.75 Intermediate Similarity NPC9639
0.7355 Intermediate Similarity NPC180462
0.7222 Intermediate Similarity NPC126634
0.719 Intermediate Similarity NPC15566
0.7165 Intermediate Similarity NPC470140
0.7 Intermediate Similarity NPC210947
0.7 Intermediate Similarity NPC470139
0.685 Remote Similarity NPC235501
0.6846 Remote Similarity NPC18223
0.6846 Remote Similarity NPC237812
0.6692 Remote Similarity NPC286696
0.6692 Remote Similarity NPC185903
0.6609 Remote Similarity NPC119133
0.6589 Remote Similarity NPC25465
0.6583 Remote Similarity NPC63433
0.6532 Remote Similarity NPC470142
0.6525 Remote Similarity NPC47936
0.6512 Remote Similarity NPC243319
0.6475 Remote Similarity NPC68938
0.6466 Remote Similarity NPC470141
0.6449 Remote Similarity NPC327477
0.6435 Remote Similarity NPC59314
0.6341 Remote Similarity NPC240084
0.6331 Remote Similarity NPC197068
0.6306 Remote Similarity NPC51000
0.6296 Remote Similarity NPC326364
0.6294 Remote Similarity NPC282531
0.6293 Remote Similarity NPC10466
0.6259 Remote Similarity NPC174020
0.6218 Remote Similarity NPC75131
0.6207 Remote Similarity NPC476561
0.6207 Remote Similarity NPC60537
0.6204 Remote Similarity NPC277608
0.62 Remote Similarity NPC100312
0.62 Remote Similarity NPC204104
0.6174 Remote Similarity NPC293163
0.6168 Remote Similarity NPC76536
0.6148 Remote Similarity NPC41958
0.6139 Remote Similarity NPC270637
0.6121 Remote Similarity NPC174114
0.6121 Remote Similarity NPC87981
0.6111 Remote Similarity NPC327579
0.6102 Remote Similarity NPC476564
0.6102 Remote Similarity NPC476099
0.608 Remote Similarity NPC278549
0.6058 Remote Similarity NPC237936
0.6055 Remote Similarity NPC262236
0.6034 Remote Similarity NPC332382
0.6 Remote Similarity NPC8590
0.5984 Remote Similarity NPC312187
0.5984 Remote Similarity NPC4837
0.5933 Remote Similarity NPC124276
0.5923 Remote Similarity NPC109322
0.5917 Remote Similarity NPC222061
0.5913 Remote Similarity NPC476128
0.5909 Remote Similarity NPC144223
0.5887 Remote Similarity NPC315642
0.5887 Remote Similarity NPC74306
0.5887 Remote Similarity NPC256849
0.5878 Remote Similarity NPC180493
0.585 Remote Similarity NPC207633
0.584 Remote Similarity NPC313547
0.5833 Remote Similarity NPC476562
0.582 Remote Similarity NPC27699
0.5797 Remote Similarity NPC320818
0.576 Remote Similarity NPC303899
0.5726 Remote Similarity NPC320256
0.5725 Remote Similarity NPC262926
0.5714 Remote Similarity NPC199790
0.5702 Remote Similarity NPC18335
0.5683 Remote Similarity NPC61198
0.5676 Remote Similarity NPC190949
0.5669 Remote Similarity NPC148385
0.5662 Remote Similarity NPC104011
0.5656 Remote Similarity NPC163105
0.5639 Remote Similarity NPC248007

  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 NPC273327 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
0.8173 Intermediate Similarity NPD8859 Approved
0.8173 Intermediate Similarity NPD8862 Approved
0.8173 Intermediate Similarity NPD8861 Approved
0.7391 Intermediate Similarity NPD9132 Discontinued
0.7355 Intermediate Similarity NPD300 Approved
0.7304 Intermediate Similarity NPD757 Phase 3
0.6846 Remote Similarity NPD9133 Approved
0.6693 Remote Similarity NPD1807 Clinical (unspecified phase)
0.6692 Remote Similarity NPD875 Clinical (unspecified phase)
0.6641 Remote Similarity NPD576 Discontinued
0.664 Remote Similarity NPD1388 Phase 1
0.664 Remote Similarity NPD1389 Clinical (unspecified phase)
0.664 Remote Similarity NPD1390 Phase 1
0.6609 Remote Similarity NPD9291 Approved
0.6593 Remote Similarity NPD9183 Clinical (unspecified phase)
0.6593 Remote Similarity NPD1451 Approved
0.6591 Remote Similarity NPD9628 Approved
0.6544 Remote Similarity NPD5342 Clinical (unspecified phase)
0.6535 Remote Similarity NPD515 Phase 1
0.6522 Remote Similarity NPD9626 Clinical (unspecified phase)
0.6512 Remote Similarity NPD9081 Clinical (unspecified phase)
0.6481 Remote Similarity NPD8787 Clinical (unspecified phase)
0.6471 Remote Similarity NPD8584 Approved
0.6458 Remote Similarity NPD2604 Approved
0.6435 Remote Similarity NPD8837 Clinical (unspecified phase)
0.6423 Remote Similarity NPD578 Discontinued
0.6422 Remote Similarity NPD8786 Approved
0.6417 Remote Similarity NPD9373 Approved
0.6371 Remote Similarity NPD307 Approved
0.6311 Remote Similarity NPD9374 Approved
0.6306 Remote Similarity NPD8838 Approved
0.6304 Remote Similarity NPD3706 Clinical (unspecified phase)
0.6304 Remote Similarity NPD174 Discontinued
0.6304 Remote Similarity NPD566 Approved
0.6304 Remote Similarity NPD567 Approved
0.6304 Remote Similarity NPD568 Approved
0.6303 Remote Similarity NPD613 Phase 2
0.6259 Remote Similarity NPD9627 Approved
0.625 Remote Similarity NPD9190 Approved
0.625 Remote Similarity NPD1731 Clinical (unspecified phase)
0.6239 Remote Similarity NPD8565 Clinical (unspecified phase)
0.6212 Remote Similarity NPD9650 Phase 3
0.6207 Remote Similarity NPD2180 Approved
0.6198 Remote Similarity NPD9375 Discontinued
0.619 Remote Similarity NPD9409 Discontinued
0.6186 Remote Similarity NPD9345 Clinical (unspecified phase)
0.6186 Remote Similarity NPD9371 Clinical (unspecified phase)
0.616 Remote Similarity NPD9606 Approved
0.616 Remote Similarity NPD9360 Approved
0.6129 Remote Similarity NPD163 Approved
0.6111 Remote Similarity NPD9607 Approved
0.6102 Remote Similarity NPD9195 Approved
0.6094 Remote Similarity NPD306 Approved
0.6068 Remote Similarity NPD9197 Discontinued
0.6058 Remote Similarity NPD8185 Discontinued
0.6058 Remote Similarity NPD8186 Phase 1
0.605 Remote Similarity NPD9196 Phase 2
0.6048 Remote Similarity NPD9086 Approved
0.6034 Remote Similarity NPD9135 Approved
0.6034 Remote Similarity NPD9255 Phase 2
0.6034 Remote Similarity NPD9134 Approved
0.6014 Remote Similarity NPD3697 Discontinued
0.6 Remote Similarity NPD1816 Clinical (unspecified phase)
0.5966 Remote Similarity NPD9502 Clinical (unspecified phase)
0.5965 Remote Similarity NPD9189 Discontinued
0.5962 Remote Similarity NPD966 Clinical (unspecified phase)
0.596 Remote Similarity NPD3130 Discontinued
0.596 Remote Similarity NPD5768 Phase 2
0.5948 Remote Similarity NPD9193 Approved
0.5948 Remote Similarity NPD9194 Approved
0.5935 Remote Similarity NPD9412 Discontinued
0.5924 Remote Similarity NPD3108 Clinical (unspecified phase)
0.5917 Remote Similarity NPD9415 Clinical (unspecified phase)
0.5891 Remote Similarity NPD2221 Clinical (unspecified phase)
0.5887 Remote Similarity NPD9359 Approved
0.5887 Remote Similarity NPD582 Approved
0.5887 Remote Similarity NPD9358 Approved
0.5882 Remote Similarity NPD340 Approved
0.5882 Remote Similarity NPD341 Approved
0.5878 Remote Similarity NPD9544 Approved
0.5878 Remote Similarity NPD78 Approved
0.5878 Remote Similarity NPD1257 Approved
0.5877 Remote Similarity NPD9101 Discontinued
0.5871 Remote Similarity NPD9582 Phase 3
0.5865 Remote Similarity NPD870 Clinical (unspecified phase)
0.5859 Remote Similarity NPD580 Discontinued
0.585 Remote Similarity NPD536 Clinical (unspecified phase)
0.5849 Remote Similarity NPD1272 Clinical (unspecified phase)
0.5833 Remote Similarity NPD281 Approved
0.5827 Remote Similarity NPD1368 Approved
0.5827 Remote Similarity NPD799 Phase 1
0.582 Remote Similarity NPD8571 Phase 3
0.5809 Remote Similarity NPD547 Clinical (unspecified phase)
0.5809 Remote Similarity NPD545 Clinical (unspecified phase)
0.5804 Remote Similarity NPD8835 Approved
0.5789 Remote Similarity NPD9366 Approved
0.5781 Remote Similarity NPD237 Clinical (unspecified phase)
0.5778 Remote Similarity NPD248 Discontinued
0.5762 Remote Similarity NPD939 Clinical (unspecified phase)
0.576 Remote Similarity NPD9182 Approved
0.5759 Remote Similarity NPD1037 Clinical (unspecified phase)
0.575 Remote Similarity NPD9629 Approved
0.5746 Remote Similarity NPD1128 Approved
0.5746 Remote Similarity NPD1354 Approved
0.5746 Remote Similarity NPD1356 Approved
0.5746 Remote Similarity NPD1355 Clinical (unspecified phase)
0.5746 Remote Similarity NPD1127 Approved
0.5725 Remote Similarity NPD194 Clinical (unspecified phase)
0.5724 Remote Similarity NPD1869 Phase 2
0.5714 Remote Similarity NPD1015 Phase 2
0.5714 Remote Similarity NPD1016 Phase 2
0.5714 Remote Similarity NPD9408 Phase 3
0.5714 Remote Similarity NPD418 Approved
0.5705 Remote Similarity NPD1027 Approved
0.5705 Remote Similarity NPD1030 Approved
0.5705 Remote Similarity NPD1029 Clinical (unspecified phase)
0.5702 Remote Similarity NPD8836 Approved
0.5696 Remote Similarity NPD3105 Discontinued
0.5692 Remote Similarity NPD9290 Approved
0.5685 Remote Similarity NPD775 Approved
0.5683 Remote Similarity NPD252 Clinical (unspecified phase)
0.5682 Remote Similarity NPD1734 Clinical (unspecified phase)
0.5672 Remote Similarity NPD1775 Approved
0.5672 Remote Similarity NPD1085 Approved
0.5667 Remote Similarity NPD2128 Phase 1
0.5652 Remote Similarity NPD9210 Phase 2
0.5652 Remote Similarity NPD209 Clinical (unspecified phase)
0.5649 Remote Similarity NPD1288 Clinical (unspecified phase)
0.5641 Remote Similarity NPD1333 Phase 3
0.5639 Remote Similarity NPD9084 Phase 2
0.563 Remote Similarity NPD2191 Discontinued
0.562 Remote Similarity NPD282 Approved
0.5612 Remote Similarity NPD1119 Phase 2
0.5606 Remote Similarity NPD4262 Discontinued
0.5603 Remote Similarity NPD1808 Phase 1
0.56 Remote Similarity NPD8954 Approved
0.56 Remote Similarity NPD8955 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