Structure

Physi-Chem Properties

Molecular Weight:  195.08
Volume:  174.534
LogP:  -0.801
LogD:  0.024
LogS:  -2.676
# Rotatable Bonds:  0
TPSA:  99.43
# H-Bond Aceptor:  7
# H-Bond Donor:  3
# Rings:  2
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.47
Synthetic Accessibility Score:  3.309
Fsp3:  0.286
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:  -5.794
MDCK Permeability:  4.778532820637338e-05
Pgp-inhibitor:  0.007
Pgp-substrate:  0.994
Human Intestinal Absorption (HIA):  0.971
20% Bioavailability (F20%):  0.011
30% Bioavailability (F30%):  0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.628
Plasma Protein Binding (PPB):  43.468772888183594%
Volume Distribution (VD):  1.212
Pgp-substrate:  48.99995803833008%

ADMET: Metabolism

CYP1A2-inhibitor:  0.044
CYP1A2-substrate:  0.981
CYP2C19-inhibitor:  0.118
CYP2C19-substrate:  0.058
CYP2C9-inhibitor:  0.016
CYP2C9-substrate:  0.027
CYP2D6-inhibitor:  0.012
CYP2D6-substrate:  0.037
CYP3A4-inhibitor:  0.006
CYP3A4-substrate:  0.675

ADMET: Excretion

Clearance (CL):  2.605
Half-life (T1/2):  0.926

ADMET: Toxicity

hERG Blockers:  0.007
Human Hepatotoxicity (H-HT):  0.764
Drug-inuced Liver Injury (DILI):  0.893
AMES Toxicity:  0.02
Rat Oral Acute Toxicity:  0.983
Maximum Recommended Daily Dose:  0.021
Skin Sensitization:  0.047
Carcinogencity:  0.076
Eye Corrosion:  0.003
Eye Irritation:  0.234
Respiratory Toxicity:  0.96

Download Data

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

  Natural Product: NPC476562

Natural Product ID:  NPC476562
Common Name*:   6-Imino-1,3-dimethyl-7,9-dihydropurine-2,8-dione;hydrochloride
IUPAC Name:   6-imino-1,3-dimethyl-7,9-dihydropurine-2,8-dione;hydrochloride
Synonyms:  
Standard InCHIKey:  JDILFQMKSZNPAJ-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C7H9N5O2.ClH/c1-11-4(8)3-5(10-6(13)9-3)12(2)7(11)14;/h8H,1-2H3,(H2,9,10,13);1H
SMILES:  CN1C2=C(C(=N)N(C1=O)C)NC(=O)N2.Cl
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   136032523
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001797] Imidazopyrimidines
        • [CHEMONTID:0000245] Purines and purine derivatives
          • [CHEMONTID:0000597] Purinones

*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
NPO33243 Amphimedon sp. Species Niphatidae Eukaryota n.a. Iojima Island, the Satsunan Islands, southern Japan (3047 N; 13017 E) n.a. PMID[15497958]
NPO33243 Amphimedon sp. Species Niphatidae Eukaryota n.a. n.a. n.a. PMID[17067172]
NPO33243 Amphimedon sp. Species Niphatidae Eukaryota n.a. Republic of Palau 2006; 2007 PMID[20681583]
NPO33243 Amphimedon sp. Species Niphatidae Eukaryota n.a. n.a. n.a. PMID[28207259]
NPO33243 Amphimedon sp. Species Niphatidae Eukaryota n.a. n.a. n.a. PMID[7714542]
NPO33243 Amphimedon sp. Species Niphatidae Eukaryota n.a. n.a. n.a. PMID[9599281]

☑ 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
NPT32 Organism Mus musculus Mus musculus Activity = 54 nmol PMID[20681583]

☑ 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 NPC476562 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
0.9388 High Similarity NPC476561
0.901 High Similarity NPC476099
0.8716 High Similarity NPC158847
0.8182 Intermediate Similarity NPC199790
0.7982 Intermediate Similarity NPC252603
0.7909 Intermediate Similarity NPC4837
0.7909 Intermediate Similarity NPC312187
0.7788 Intermediate Similarity NPC148385
0.7778 Intermediate Similarity NPC476564
0.7768 Intermediate Similarity NPC41958
0.7768 Intermediate Similarity NPC303899
0.7652 Intermediate Similarity NPC278549
0.7523 Intermediate Similarity NPC10466
0.7411 Intermediate Similarity NPC75131
0.7383 Intermediate Similarity NPC320256
0.7304 Intermediate Similarity NPC256849
0.7297 Intermediate Similarity NPC18335
0.7232 Intermediate Similarity NPC119133
0.72 Intermediate Similarity NPC246193
0.713 Intermediate Similarity NPC47936
0.7091 Intermediate Similarity NPC293163
0.7054 Intermediate Similarity NPC59314
0.7027 Intermediate Similarity NPC87981
0.7027 Intermediate Similarity NPC174114
0.6992 Remote Similarity NPC109322
0.6944 Remote Similarity NPC51000
0.6935 Remote Similarity NPC180493
0.6911 Remote Similarity NPC5707
0.6797 Remote Similarity NPC287876
0.6719 Remote Similarity NPC14330
0.6692 Remote Similarity NPC57279
0.6667 Remote Similarity NPC313547
0.6667 Remote Similarity NPC104011
0.6639 Remote Similarity NPC68938
0.6639 Remote Similarity NPC189314
0.656 Remote Similarity NPC139776
0.6406 Remote Similarity NPC248007
0.6283 Remote Similarity NPC9639
0.627 Remote Similarity NPC327579
0.626 Remote Similarity NPC327613
0.6218 Remote Similarity NPC155498
0.6096 Remote Similarity NPC321052
0.6058 Remote Similarity NPC320818
0.605 Remote Similarity NPC111132
0.6 Remote Similarity NPC317821
0.5971 Remote Similarity NPC33996
0.5929 Remote Similarity NPC129756
0.5887 Remote Similarity NPC226184
0.5887 Remote Similarity NPC167285
0.5887 Remote Similarity NPC76544
0.5887 Remote Similarity NPC209525
0.5887 Remote Similarity NPC161659
0.5839 Remote Similarity NPC324009
0.5833 Remote Similarity NPC273327
0.5804 Remote Similarity NPC314152
0.5804 Remote Similarity NPC229974
0.5797 Remote Similarity NPC319221
0.5793 Remote Similarity NPC164665
0.5793 Remote Similarity NPC197068
0.5793 Remote Similarity NPC189068
0.5753 Remote Similarity NPC219313
0.5753 Remote Similarity NPC309832
0.575 Remote Similarity NPC187191
0.575 Remote Similarity NPC326248
0.5736 Remote Similarity NPC240084
0.5724 Remote Similarity NPC107374
0.5724 Remote Similarity NPC21448
0.5724 Remote Similarity NPC156461
0.5703 Remote Similarity NPC63433
0.5693 Remote Similarity NPC243319
0.5676 Remote Similarity NPC136349
0.5672 Remote Similarity NPC15566
0.5646 Remote Similarity NPC269827
0.5643 Remote Similarity NPC262926
0.5608 Remote Similarity NPC121222
0.5603 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 NPC476562 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
0.7982 Intermediate Similarity NPD9288 Approved
0.7982 Intermediate Similarity NPD76 Approved
0.7982 Intermediate Similarity NPD9289 Approved
0.7982 Intermediate Similarity NPD9292 Approved
0.7647 Intermediate Similarity NPD579 Clinical (unspecified phase)
0.7586 Intermediate Similarity NPD237 Clinical (unspecified phase)
0.7586 Intermediate Similarity NPD9360 Approved
0.7304 Intermediate Similarity NPD9358 Approved
0.7304 Intermediate Similarity NPD9359 Approved
0.7297 Intermediate Similarity NPD8836 Approved
0.7232 Intermediate Similarity NPD9291 Approved
0.713 Intermediate Similarity NPD8955 Approved
0.713 Intermediate Similarity NPD8954 Approved
0.7099 Intermediate Similarity NPD1118 Discontinued
0.7054 Intermediate Similarity NPD8837 Clinical (unspecified phase)
0.6992 Remote Similarity NPD1117 Clinical (unspecified phase)
0.6944 Remote Similarity NPD8838 Approved
0.6942 Remote Similarity NPD580 Discontinued
0.6935 Remote Similarity NPD78 Approved
0.6935 Remote Similarity NPD9544 Approved
0.6911 Remote Similarity NPD8830 Phase 3
0.6891 Remote Similarity NPD9086 Approved
0.688 Remote Similarity NPD281 Approved
0.6829 Remote Similarity NPD2221 Clinical (unspecified phase)
0.6797 Remote Similarity NPD8829 Clinical (unspecified phase)
0.6774 Remote Similarity NPD4262 Discontinued
0.6772 Remote Similarity NPD1127 Approved
0.6772 Remote Similarity NPD1128 Approved
0.6741 Remote Similarity NPD2179 Discontinued
0.6721 Remote Similarity NPD578 Discontinued
0.6641 Remote Similarity NPD9083 Clinical (unspecified phase)
0.6639 Remote Similarity NPD8833 Approved
0.6639 Remote Similarity NPD8831 Approved
0.6615 Remote Similarity NPD282 Approved
0.6583 Remote Similarity NPD9373 Approved
0.6562 Remote Similarity NPD1085 Approved
0.6562 Remote Similarity NPD1775 Approved
0.65 Remote Similarity NPD4183 Phase 3
0.65 Remote Similarity NPD4182 Phase 3
0.65 Remote Similarity NPD9375 Discontinued
0.6475 Remote Similarity NPD9374 Approved
0.6466 Remote Similarity NPD9484 Clinical (unspecified phase)
0.6466 Remote Similarity NPD1119 Phase 2
0.6406 Remote Similarity NPD9084 Phase 2
0.6385 Remote Similarity NPD870 Clinical (unspecified phase)
0.6357 Remote Similarity NPD9408 Phase 3
0.6349 Remote Similarity NPD9290 Approved
0.6336 Remote Similarity NPD9633 Phase 3
0.632 Remote Similarity NPD9606 Approved
0.6312 Remote Similarity NPD7531 Clinical (unspecified phase)
0.6284 Remote Similarity NPD5321 Phase 3
0.627 Remote Similarity NPD307 Approved
0.627 Remote Similarity NPD9607 Approved
0.622 Remote Similarity NPD9409 Discontinued
0.621 Remote Similarity NPD757 Phase 3
0.6187 Remote Similarity NPD2253 Discontinued
0.6186 Remote Similarity NPD340 Approved
0.6186 Remote Similarity NPD341 Approved
0.6176 Remote Similarity NPD535 Approved
0.6165 Remote Similarity NPD248 Discontinued
0.6134 Remote Similarity NPD9626 Clinical (unspecified phase)
0.605 Remote Similarity NPD8859 Approved
0.605 Remote Similarity NPD8861 Approved
0.605 Remote Similarity NPD8862 Approved
0.6029 Remote Similarity NPD209 Clinical (unspecified phase)
0.6014 Remote Similarity NPD1730 Discontinued
0.5986 Remote Similarity NPD9704 Approved
0.5959 Remote Similarity NPD3708 Phase 2
0.594 Remote Similarity NPD515 Phase 1
0.5902 Remote Similarity NPD1816 Clinical (unspecified phase)
0.5893 Remote Similarity NPD9103 Approved
0.5893 Remote Similarity NPD9102 Approved
0.5887 Remote Similarity NPD193 Suspended
0.5887 Remote Similarity NPD3695 Approved
0.5887 Remote Similarity NPD3696 Approved
0.5827 Remote Similarity NPD1121 Approved
0.5827 Remote Similarity NPD1120 Approved
0.5821 Remote Similarity NPD300 Approved
0.5804 Remote Similarity NPD185 Approved
0.5797 Remote Similarity NPD1058 Discontinued
0.5786 Remote Similarity NPD9550 Approved
0.5786 Remote Similarity NPD9551 Approved
0.5764 Remote Similarity NPD4240 Approved
0.5745 Remote Similarity NPD1808 Phase 1
0.5736 Remote Similarity NPD1368 Approved
0.5725 Remote Similarity NPD547 Clinical (unspecified phase)
0.5725 Remote Similarity NPD545 Clinical (unspecified phase)
0.5724 Remote Similarity NPD7158 Phase 1
0.5724 Remote Similarity NPD250 Approved
0.5724 Remote Similarity NPD249 Approved
0.5724 Remote Similarity NPD166 Approved
0.5703 Remote Similarity NPD9584 Phase 2
0.5693 Remote Similarity NPD9081 Clinical (unspecified phase)
0.5687 Remote Similarity NPD3081 Clinical (unspecified phase)
0.5676 Remote Similarity NPD548 Clinical (unspecified phase)
0.5646 Remote Similarity NPD195 Approved
0.5646 Remote Similarity NPD186 Discovery
0.5643 Remote Similarity NPD194 Clinical (unspecified phase)
0.5625 Remote Similarity NPD1431 Approved
0.5625 Remote Similarity NPD1430 Approved
0.5616 Remote Similarity NPD171 Discontinued
0.5603 Remote Similarity NPD252 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