Structure

Physi-Chem Properties

Molecular Weight:  181.05
Volume:  161.331
LogP:  -0.807
LogD:  -0.428
LogS:  -0.824
# Rotatable Bonds:  1
TPSA:  90.62
# H-Bond Aceptor:  6
# H-Bond Donor:  3
# Rings:  2
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.492
Synthetic Accessibility Score:  3.561
Fsp3:  0.143
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.057
MDCK Permeability:  0.00024847747408784926
Pgp-inhibitor:  0.0
Pgp-substrate:  0.04
Human Intestinal Absorption (HIA):  0.019
20% Bioavailability (F20%):  0.144
30% Bioavailability (F30%):  0.376

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.806
Plasma Protein Binding (PPB):  14.703968048095703%
Volume Distribution (VD):  0.812
Pgp-substrate:  78.44215393066406%

ADMET: Metabolism

CYP1A2-inhibitor:  0.024
CYP1A2-substrate:  0.943
CYP2C19-inhibitor:  0.026
CYP2C19-substrate:  0.057
CYP2C9-inhibitor:  0.006
CYP2C9-substrate:  0.11
CYP2D6-inhibitor:  0.007
CYP2D6-substrate:  0.102
CYP3A4-inhibitor:  0.019
CYP3A4-substrate:  0.094

ADMET: Excretion

Clearance (CL):  4.154
Half-life (T1/2):  0.922

ADMET: Toxicity

hERG Blockers:  0.018
Human Hepatotoxicity (H-HT):  0.827
Drug-inuced Liver Injury (DILI):  0.951
AMES Toxicity:  0.018
Rat Oral Acute Toxicity:  0.004
Maximum Recommended Daily Dose:  0.851
Skin Sensitization:  0.155
Carcinogencity:  0.651
Eye Corrosion:  0.003
Eye Irritation:  0.039
Respiratory Toxicity:  0.314

Download Data

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

  Natural Product: NPC470138

Natural Product ID:  NPC470138
Common Name*:   5-Oxo-7,8-Dihydro-6H-Imidazo[1,5-C]Pyrimidine-7-Carboxylic Acid
IUPAC Name:   5-oxo-7,8-dihydro-6H-imidazo[1,5-c]pyrimidine-7-carboxylic acid
Synonyms:  
Standard InCHIKey:  QRHVJFJTKLUIDU-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C7H7N3O3/c11-6(12)5-1-4-2-8-3-10(4)7(13)9-5/h2-3,5H,1H2,(H,9,13)(H,11,12)
SMILES:  C1C(NC(=O)N2C1=CN=C2)C(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1780249
PubChem CID:   11286826
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0000013] Amino acids, peptides, and analogues
          • [CHEMONTID:0000347] Amino acids and derivatives
            • [CHEMONTID:0000060] Alpha amino acids 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
NPO9032 Geotrichum candidum Species Dipodascaceae Eukaryota n.a. n.a. n.a. PMID[20488699]
NPO9032 Geotrichum candidum Species Dipodascaceae 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 = 3560.0 nM PMID[547735]

☑ 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 NPC470138 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
0.9286 High Similarity NPC126634
0.9062 High Similarity NPC470140
0.9 High Similarity NPC210947
0.8855 High Similarity NPC470139
0.8846 High Similarity NPC237812
0.8846 High Similarity NPC18223
0.8647 High Similarity NPC286696
0.8647 High Similarity NPC185903
0.8629 High Similarity NPC470142
0.8462 Intermediate Similarity NPC235501
0.8333 Intermediate Similarity NPC327477
0.8284 Intermediate Similarity NPC470141
0.8045 Intermediate Similarity NPC25465
0.7833 Intermediate Similarity NPC273327
0.7746 Intermediate Similarity NPC174020
0.7744 Intermediate Similarity NPC180462
0.7635 Intermediate Similarity NPC60537
0.7463 Intermediate Similarity NPC15566
0.6905 Remote Similarity NPC326248
0.6905 Remote Similarity NPC187191
0.6842 Remote Similarity NPC327613
0.6667 Remote Similarity NPC124276
0.6565 Remote Similarity NPC155498
0.6538 Remote Similarity NPC111132
0.6292 Remote Similarity NPC313504
0.6149 Remote Similarity NPC243319
0.6054 Remote Similarity NPC144223
0.6026 Remote Similarity NPC315642
0.6026 Remote Similarity NPC74306
0.6022 Remote Similarity NPC54537
0.6014 Remote Similarity NPC47936
0.6 Remote Similarity NPC9639
0.5988 Remote Similarity NPC207633
0.5956 Remote Similarity NPC119133
0.5948 Remote Similarity NPC320818
0.5918 Remote Similarity NPC180493
0.5882 Remote Similarity NPC262926
0.5845 Remote Similarity NPC63433
0.5844 Remote Similarity NPC61198
0.5823 Remote Similarity NPC8590
0.5793 Remote Similarity NPC282531
0.5761 Remote Similarity NPC201900
0.5755 Remote Similarity NPC75131
0.5744 Remote Similarity NPC477419
0.5744 Remote Similarity NPC477417
0.5723 Remote Similarity NPC290959
0.5693 Remote Similarity NPC10466
0.5678 Remote Similarity NPC238945
0.566 Remote Similarity NPC186619
0.5659 Remote Similarity NPC323244
0.5655 Remote Similarity NPC240084
0.5655 Remote Similarity NPC278549
0.5649 Remote Similarity NPC324009
0.5638 Remote Similarity NPC109322
0.5613 Remote Similarity NPC319221
0.5604 Remote Similarity NPC477118
0.5602 Remote Similarity NPC321052

  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 NPC470138 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
0.8846 High Similarity NPD9133 Approved
0.8421 Intermediate Similarity NPD9628 Approved
0.8382 Intermediate Similarity NPD9183 Clinical (unspecified phase)
0.8248 Intermediate Similarity NPD1451 Approved
0.8235 Intermediate Similarity NPD875 Clinical (unspecified phase)
0.8 Intermediate Similarity NPD9627 Approved
0.7891 Intermediate Similarity NPD2604 Approved
0.7744 Intermediate Similarity NPD300 Approved
0.7635 Intermediate Similarity NPD2180 Approved
0.7568 Intermediate Similarity NPD1731 Clinical (unspecified phase)
0.7552 Intermediate Similarity NPD567 Approved
0.7552 Intermediate Similarity NPD568 Approved
0.7552 Intermediate Similarity NPD566 Approved
0.7417 Intermediate Similarity NPD3697 Discontinued
0.7358 Intermediate Similarity NPD3108 Clinical (unspecified phase)
0.7338 Intermediate Similarity NPD3130 Discontinued
0.7075 Intermediate Similarity NPD5342 Clinical (unspecified phase)
0.6914 Remote Similarity NPD3105 Discontinued
0.6828 Remote Similarity NPD576 Discontinued
0.6741 Remote Similarity NPD9132 Discontinued
0.6687 Remote Similarity NPD5768 Phase 2
0.6566 Remote Similarity NPD1037 Clinical (unspecified phase)
0.6538 Remote Similarity NPD8859 Approved
0.6538 Remote Similarity NPD8862 Approved
0.6538 Remote Similarity NPD8861 Approved
0.6519 Remote Similarity NPD3497 Clinical (unspecified phase)
0.6405 Remote Similarity NPD3706 Clinical (unspecified phase)
0.6266 Remote Similarity NPD3708 Phase 2
0.619 Remote Similarity NPD1807 Clinical (unspecified phase)
0.6187 Remote Similarity NPD757 Phase 3
0.6184 Remote Similarity NPD1808 Phase 1
0.6149 Remote Similarity NPD9081 Clinical (unspecified phase)
0.6114 Remote Similarity NPD2137 Approved
0.6114 Remote Similarity NPD2138 Approved
0.6087 Remote Similarity NPD536 Clinical (unspecified phase)
0.6067 Remote Similarity NPD547 Clinical (unspecified phase)
0.6054 Remote Similarity NPD515 Phase 1
0.6053 Remote Similarity NPD1120 Approved
0.6053 Remote Similarity NPD1121 Approved
0.6038 Remote Similarity NPD775 Approved
0.6027 Remote Similarity NPD1390 Phase 1
0.6027 Remote Similarity NPD1388 Phase 1
0.6027 Remote Similarity NPD1389 Clinical (unspecified phase)
0.6026 Remote Similarity NPD582 Approved
0.6025 Remote Similarity NPD7842 Phase 2
0.6021 Remote Similarity NPD8261 Discontinued
0.5987 Remote Similarity NPD1119 Phase 2
0.5964 Remote Similarity NPD1335 Approved
0.596 Remote Similarity NPD545 Clinical (unspecified phase)
0.5956 Remote Similarity NPD9291 Approved
0.5944 Remote Similarity NPD578 Discontinued
0.5938 Remote Similarity NPD7465 Suspended
0.5928 Remote Similarity NPD7557 Clinical (unspecified phase)
0.5918 Remote Similarity NPD9544 Approved
0.5918 Remote Similarity NPD78 Approved
0.5906 Remote Similarity NPD9582 Phase 3
0.5903 Remote Similarity NPD307 Approved
0.5896 Remote Similarity NPD966 Clinical (unspecified phase)
0.5882 Remote Similarity NPD194 Clinical (unspecified phase)
0.5882 Remote Similarity NPD9626 Clinical (unspecified phase)
0.5866 Remote Similarity NPD7246 Clinical (unspecified phase)
0.5866 Remote Similarity NPD7245 Approved
0.586 Remote Similarity NPD1430 Approved
0.586 Remote Similarity NPD1431 Approved
0.5844 Remote Similarity NPD252 Clinical (unspecified phase)
0.5839 Remote Similarity NPD1085 Approved
0.5839 Remote Similarity NPD1775 Approved
0.5818 Remote Similarity NPD510 Phase 1
0.5795 Remote Similarity NPD1272 Clinical (unspecified phase)
0.5786 Remote Similarity NPD174 Discontinued
0.5784 Remote Similarity NPD8641 Approved
0.5778 Remote Similarity NPD1308 Approved
0.5764 Remote Similarity NPD1368 Approved
0.5759 Remote Similarity NPD2253 Discontinued
0.5737 Remote Similarity NPD2807 Discontinued
0.5724 Remote Similarity NPD9632 Phase 3
0.5714 Remote Similarity NPD613 Phase 2
0.5714 Remote Similarity NPD209 Clinical (unspecified phase)
0.5696 Remote Similarity NPD549 Approved
0.5695 Remote Similarity NPD870 Clinical (unspecified phase)
0.5685 Remote Similarity NPD4341 Clinical (unspecified phase)
0.5678 Remote Similarity NPD8271 Discontinued
0.5671 Remote Similarity NPD962 Phase 3
0.5659 Remote Similarity NPD8292 Phase 2
0.5625 Remote Similarity NPD9086 Approved
0.5625 Remote Similarity NPD1117 Clinical (unspecified phase)
0.5625 Remote Similarity NPD9374 Approved
0.5625 Remote Similarity NPD2618 Phase 1
0.5621 Remote Similarity NPD248 Discontinued
0.5616 Remote Similarity NPD9360 Approved
0.5615 Remote Similarity NPD8113 Phase 2
0.5605 Remote Similarity NPD2602 Clinical (unspecified phase)

  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