Structure

Physi-Chem Properties

Molecular Weight:  243.09
Volume:  216.139
LogP:  -1.127
LogD:  -1.165
LogS:  -0.54
# Rotatable Bonds:  2
TPSA:  117.44
# H-Bond Aceptor:  8
# H-Bond Donor:  3
# Rings:  2
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.546
Synthetic Accessibility Score:  3.723
Fsp3:  0.667
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.786
MDCK Permeability:  2.8911716071888804e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.064
Human Intestinal Absorption (HIA):  0.054
20% Bioavailability (F20%):  0.008
30% Bioavailability (F30%):  0.018

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.378
Plasma Protein Binding (PPB):  16.206302642822266%
Volume Distribution (VD):  0.587
Pgp-substrate:  74.91453552246094%

ADMET: Metabolism

CYP1A2-inhibitor:  0.01
CYP1A2-substrate:  0.098
CYP2C19-inhibitor:  0.02
CYP2C19-substrate:  0.06
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.385
CYP2D6-inhibitor:  0.006
CYP2D6-substrate:  0.094
CYP3A4-inhibitor:  0.004
CYP3A4-substrate:  0.112

ADMET: Excretion

Clearance (CL):  7.447
Half-life (T1/2):  0.858

ADMET: Toxicity

hERG Blockers:  0.012
Human Hepatotoxicity (H-HT):  0.84
Drug-inuced Liver Injury (DILI):  0.984
AMES Toxicity:  0.38
Rat Oral Acute Toxicity:  0.011
Maximum Recommended Daily Dose:  0.026
Skin Sensitization:  0.047
Carcinogencity:  0.087
Eye Corrosion:  0.003
Eye Irritation:  0.025
Respiratory Toxicity:  0.018

Download Data

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

  Natural Product: NPC319753

Natural Product ID:  NPC319753
Common Name*:   2-[(2R,4S,5R)-4-Hydroxy-5-(Hydroxymethyl)Oxolan-2-Yl]-6-Methyl-1,2,4-Triazine-3,5-Dione
IUPAC Name:   2-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-6-methyl-1,2,4-triazine-3,5-dione
Synonyms:  
Standard InCHIKey:  LXHOFEUVCQUXRZ-RRKCRQDMSA-N
Standard InCHI:  InChI=1S/C9H13N3O5/c1-4-8(15)10-9(16)12(11-4)7-2-5(14)6(3-13)17-7/h5-7,13-14H,2-3H2,1H3,(H,10,15,16)/t5-,6+,7+/m0/s1
SMILES:  OC[C@H]1O[C@H](C[C@@H]1O)n1nc(C)c(nc1=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL463659
PubChem CID:   96565
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000098] Triazines
        • [CHEMONTID:0004107] 1,2,4-triazines

*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
NPO30193 Mycoplasma genitalium Species Mycoplasmataceae Bacteria n.a. n.a. n.a. PMID[22817898]

☑ 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
NPT2873 Individual Protein Thymidine phosphorylase Escherichia coli K-12 Activity = 5.4 % PMID[498293]
NPT2873 Individual Protein Thymidine phosphorylase Escherichia coli K-12 Activity = 7.9 % PMID[498293]

☑ 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 NPC319753 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
0.825 Intermediate Similarity NPC325902
0.8125 Intermediate Similarity NPC329077
0.7841 Intermediate Similarity NPC109188
0.7586 Intermediate Similarity NPC325723
0.7471 Intermediate Similarity NPC112842
0.7471 Intermediate Similarity NPC71339
0.7356 Intermediate Similarity NPC106780
0.7222 Intermediate Similarity NPC163352
0.7222 Intermediate Similarity NPC210456
0.7111 Intermediate Similarity NPC43246
0.7111 Intermediate Similarity NPC89051
0.7065 Intermediate Similarity NPC171116
0.6915 Remote Similarity NPC327344
0.6882 Remote Similarity NPC315063
0.6809 Remote Similarity NPC324390
0.6771 Remote Similarity NPC324516
0.6771 Remote Similarity NPC318166
0.6737 Remote Similarity NPC322594
0.6737 Remote Similarity NPC320249
0.6598 Remote Similarity NPC17892
0.6598 Remote Similarity NPC36985
0.6531 Remote Similarity NPC73765
0.6531 Remote Similarity NPC283698
0.6512 Remote Similarity NPC315806
0.6364 Remote Similarity NPC317639
0.617 Remote Similarity NPC229249
0.6136 Remote Similarity NPC126186
0.6133 Remote Similarity NPC224624
0.6082 Remote Similarity NPC328806
0.6 Remote Similarity NPC470782
0.5979 Remote Similarity NPC190334
0.5979 Remote Similarity NPC62927
0.593 Remote Similarity NPC316445
0.5926 Remote Similarity NPC329277
0.5893 Remote Similarity NPC478024
0.5818 Remote Similarity NPC149843
0.5818 Remote Similarity NPC155087
0.573 Remote Similarity NPC470781
0.5684 Remote Similarity NPC470783
0.5679 Remote Similarity NPC293551
0.5638 Remote Similarity NPC312315
0.5631 Remote Similarity NPC329384
0.5618 Remote Similarity NPC223174
0.5618 Remote Similarity NPC327486
0.5618 Remote Similarity NPC327753

  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 NPC319753 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
0.7841 Intermediate Similarity NPD1331 Approved
0.7471 Intermediate Similarity NPD280 Approved
0.7326 Intermediate Similarity NPD9556 Approved
0.7303 Intermediate Similarity NPD240 Phase 3
0.7241 Intermediate Similarity NPD9560 Approved
0.7241 Intermediate Similarity NPD9561 Approved
0.7191 Intermediate Similarity NPD9557 Clinical (unspecified phase)
0.7159 Intermediate Similarity NPD9546 Phase 2
0.7159 Intermediate Similarity NPD9559 Phase 1
0.7111 Intermediate Similarity NPD9580 Clinical (unspecified phase)
0.7111 Intermediate Similarity NPD170 Approved
0.7111 Intermediate Similarity NPD9581 Clinical (unspecified phase)
0.7097 Intermediate Similarity NPD251 Approved
0.7079 Intermediate Similarity NPD9533 Phase 2
0.7079 Intermediate Similarity NPD238 Clinical (unspecified phase)
0.7079 Intermediate Similarity NPD239 Phase 2
0.7065 Intermediate Similarity NPD755 Phase 3
0.7065 Intermediate Similarity NPD841 Approved
0.7045 Intermediate Similarity NPD2691 Clinical (unspecified phase)
0.6989 Remote Similarity NPD9565 Discontinued
0.6932 Remote Similarity NPD9558 Phase 3
0.6923 Remote Similarity NPD9562 Discovery
0.6778 Remote Similarity NPD9529 Phase 1
0.6633 Remote Similarity NPD762 Discontinued
0.6598 Remote Similarity NPD501 Phase 1
0.6588 Remote Similarity NPD9405 Approved
0.6531 Remote Similarity NPD9639 Clinical (unspecified phase)
0.6512 Remote Similarity NPD9653 Clinical (unspecified phase)
0.6489 Remote Similarity NPD1760 Approved
0.6489 Remote Similarity NPD241 Discontinued
0.6444 Remote Similarity NPD9429 Discontinued
0.64 Remote Similarity NPD502 Approved
0.6364 Remote Similarity NPD9407 Approved
0.6337 Remote Similarity NPD5789 Clinical (unspecified phase)
0.6327 Remote Similarity NPD1686 Approved
0.617 Remote Similarity NPD9601 Approved
0.6129 Remote Similarity NPD9573 Phase 2
0.6117 Remote Similarity NPD223 Clinical (unspecified phase)
0.6095 Remote Similarity NPD1061 Clinical (unspecified phase)
0.6075 Remote Similarity NPD1385 Discontinued
0.6061 Remote Similarity NPD9585 Discontinued
0.6024 Remote Similarity NPD9211 Clinical (unspecified phase)
0.5981 Remote Similarity NPD3128 Phase 3
0.5979 Remote Similarity NPD9602 Phase 3
0.5979 Remote Similarity NPD9604 Approved
0.5979 Remote Similarity NPD9603 Phase 3
0.596 Remote Similarity NPD267 Discontinued
0.5938 Remote Similarity NPD9555 Phase 2
0.5926 Remote Similarity NPD3129 Phase 3
0.5918 Remote Similarity NPD9553 Approved
0.5918 Remote Similarity NPD9554 Approved
0.59 Remote Similarity NPD6943 Clinical (unspecified phase)
0.59 Remote Similarity NPD285 Discontinued
0.5851 Remote Similarity NPD9600 Approved
0.5758 Remote Similarity NPD301 Discontinued
0.5729 Remote Similarity NPD9572 Clinical (unspecified phase)
0.5701 Remote Similarity NPD7651 Approved
0.5686 Remote Similarity NPD279 Clinical (unspecified phase)
0.5631 Remote Similarity NPD215 Discontinued
0.5618 Remote Similarity NPD9445 Approved
0.5614 Remote Similarity NPD7914 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