Structure

Physi-Chem Properties

Molecular Weight:  432.84
Volume:  211.884
LogP:  0.901
LogD:  0.564
LogS:  -2.129
# Rotatable Bonds:  1
TPSA:  90.62
# H-Bond Aceptor:  6
# H-Bond Donor:  3
# Rings:  2
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.444
Synthetic Accessibility Score:  4.007
Fsp3:  0.143
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.856
MDCK Permeability:  4.4845226511824876e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.506
Human Intestinal Absorption (HIA):  0.398
20% Bioavailability (F20%):  0.009
30% Bioavailability (F30%):  0.823

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.248
Plasma Protein Binding (PPB):  62.059139251708984%
Volume Distribution (VD):  0.721
Pgp-substrate:  46.678985595703125%

ADMET: Metabolism

CYP1A2-inhibitor:  0.122
CYP1A2-substrate:  0.853
CYP2C19-inhibitor:  0.013
CYP2C19-substrate:  0.065
CYP2C9-inhibitor:  0.006
CYP2C9-substrate:  0.095
CYP2D6-inhibitor:  0.018
CYP2D6-substrate:  0.133
CYP3A4-inhibitor:  0.007
CYP3A4-substrate:  0.123

ADMET: Excretion

Clearance (CL):  4.306
Half-life (T1/2):  0.919

ADMET: Toxicity

hERG Blockers:  0.005
Human Hepatotoxicity (H-HT):  0.132
Drug-inuced Liver Injury (DILI):  0.049
AMES Toxicity:  0.022
Rat Oral Acute Toxicity:  0.004
Maximum Recommended Daily Dose:  0.822
Skin Sensitization:  0.052
Carcinogencity:  0.743
Eye Corrosion:  0.003
Eye Irritation:  0.049
Respiratory Toxicity:  0.845

Download Data

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

  Natural Product: NPC470142

Natural Product ID:  NPC470142
Common Name*:   1,3-Diiodo-5-Oxo-7,8-Dihydro-6H-Imidazo[1,5-C]Pyrimidine-7-Carboxylic Acid
IUPAC Name:   1,3-diiodo-5-oxo-7,8-dihydro-6H-imidazo[1,5-c]pyrimidine-7-carboxylic acid
Synonyms:  
Standard InCHIKey:  QBFIEHVTLLEHLU-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C7H5I2N3O3/c8-4-3-1-2(5(13)14)10-7(15)12(3)6(9)11-4/h2H,1H2,(H,10,15)(H,13,14)
SMILES:  C1C(NC(=O)N2C1=C(N=C2I)I)C(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1780254
PubChem CID:   54587588
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 = 58700.0 nM PMID[573542]

☑ 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 NPC470142 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
0.8629 High Similarity NPC470138
0.8154 Intermediate Similarity NPC470141
0.8 Intermediate Similarity NPC126634
0.7803 Intermediate Similarity NPC470140
0.7761 Intermediate Similarity NPC210947
0.763 Intermediate Similarity NPC470139
0.7612 Intermediate Similarity NPC237812
0.7612 Intermediate Similarity NPC18223
0.7445 Intermediate Similarity NPC286696
0.7445 Intermediate Similarity NPC185903
0.7239 Intermediate Similarity NPC235501
0.7183 Intermediate Similarity NPC327477
0.6861 Remote Similarity NPC25465
0.6644 Remote Similarity NPC174020
0.6579 Remote Similarity NPC60537
0.6569 Remote Similarity NPC180462
0.6532 Remote Similarity NPC273327
0.6304 Remote Similarity NPC15566
0.5909 Remote Similarity NPC75131
0.5855 Remote Similarity NPC74306
0.5855 Remote Similarity NPC315642
0.5846 Remote Similarity NPC10466
0.5821 Remote Similarity NPC47936
0.5802 Remote Similarity NPC124276
0.5782 Remote Similarity NPC324009
0.5772 Remote Similarity NPC320818
0.5758 Remote Similarity NPC119133
0.5743 Remote Similarity NPC319221
0.5734 Remote Similarity NPC180493
0.5705 Remote Similarity NPC262926
0.5693 Remote Similarity NPC327613
0.5692 Remote Similarity NPC326248
0.5692 Remote Similarity NPC187191
0.5667 Remote Similarity NPC61198

  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 NPC470142 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
0.7612 Intermediate Similarity NPD9133 Approved
0.7226 Intermediate Similarity NPD9628 Approved
0.7214 Intermediate Similarity NPD9183 Clinical (unspecified phase)
0.7092 Intermediate Similarity NPD1451 Approved
0.7071 Intermediate Similarity NPD875 Clinical (unspecified phase)
0.6875 Remote Similarity NPD9627 Approved
0.6821 Remote Similarity NPD2604 Approved
0.6579 Remote Similarity NPD2180 Approved
0.6569 Remote Similarity NPD300 Approved
0.6513 Remote Similarity NPD1731 Clinical (unspecified phase)
0.6463 Remote Similarity NPD566 Approved
0.6463 Remote Similarity NPD568 Approved
0.6463 Remote Similarity NPD567 Approved
0.6387 Remote Similarity NPD3697 Discontinued
0.638 Remote Similarity NPD3108 Clinical (unspecified phase)
0.6329 Remote Similarity NPD3130 Discontinued
0.6104 Remote Similarity NPD3708 Phase 2
0.6026 Remote Similarity NPD5342 Clinical (unspecified phase)
0.6014 Remote Similarity NPD1808 Phase 1
0.5964 Remote Similarity NPD3105 Discontinued
0.589 Remote Similarity NPD547 Clinical (unspecified phase)
0.5878 Remote Similarity NPD1121 Approved
0.5878 Remote Similarity NPD1120 Approved
0.586 Remote Similarity NPD7842 Phase 2
0.5855 Remote Similarity NPD582 Approved
0.5811 Remote Similarity NPD1119 Phase 2
0.5782 Remote Similarity NPD545 Clinical (unspecified phase)
0.578 Remote Similarity NPD2138 Approved
0.578 Remote Similarity NPD2137 Approved
0.5772 Remote Similarity NPD576 Discontinued
0.5758 Remote Similarity NPD9291 Approved
0.5755 Remote Similarity NPD237 Clinical (unspecified phase)
0.5755 Remote Similarity NPD578 Discontinued
0.5734 Remote Similarity NPD9544 Approved
0.5734 Remote Similarity NPD78 Approved
0.5732 Remote Similarity NPD5768 Phase 2
0.5714 Remote Similarity NPD307 Approved
0.5705 Remote Similarity NPD194 Clinical (unspecified phase)
0.5686 Remote Similarity NPD1431 Approved
0.5686 Remote Similarity NPD1430 Approved
0.5682 Remote Similarity NPD9626 Clinical (unspecified phase)
0.5676 Remote Similarity NPD3497 Clinical (unspecified phase)
0.5669 Remote Similarity NPD775 Approved
0.5667 Remote Similarity NPD252 Clinical (unspecified phase)
0.5655 Remote Similarity NPD1775 Approved
0.5655 Remote Similarity NPD1085 Approved
0.5647 Remote Similarity NPD1037 Clinical (unspecified phase)
0.5625 Remote Similarity NPD536 Clinical (unspecified phase)
0.5621 Remote Similarity NPD1118 Discontinued
0.5612 Remote Similarity NPD9132 Discontinued

  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