Structure

Physi-Chem Properties

Molecular Weight:  324.07
Volume:  271.273
LogP:  -1.81
LogD:  -1.353
LogS:  0.048
# Rotatable Bonds:  4
TPSA:  142.47
# H-Bond Aceptor:  10
# H-Bond Donor:  3
# Rings:  2
# Heavy Atoms:  11

MedChem Properties

QED Drug-Likeness Score:  0.555
Synthetic Accessibility Score:  5.041
Fsp3:  0.8
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:  -5.967
MDCK Permeability:  7.363980694208294e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.174
Human Intestinal Absorption (HIA):  0.309
20% Bioavailability (F20%):  0.453
30% Bioavailability (F30%):  0.675

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.381
Plasma Protein Binding (PPB):  11.871406555175781%
Volume Distribution (VD):  0.396
Pgp-substrate:  81.40642547607422%

ADMET: Metabolism

CYP1A2-inhibitor:  0.003
CYP1A2-substrate:  0.061
CYP2C19-inhibitor:  0.062
CYP2C19-substrate:  0.05
CYP2C9-inhibitor:  0.008
CYP2C9-substrate:  0.349
CYP2D6-inhibitor:  0.114
CYP2D6-substrate:  0.121
CYP3A4-inhibitor:  0.005
CYP3A4-substrate:  0.018

ADMET: Excretion

Clearance (CL):  1.733
Half-life (T1/2):  0.909

ADMET: Toxicity

hERG Blockers:  0.014
Human Hepatotoxicity (H-HT):  0.342
Drug-inuced Liver Injury (DILI):  0.533
AMES Toxicity:  0.054
Rat Oral Acute Toxicity:  0.006
Maximum Recommended Daily Dose:  0.935
Skin Sensitization:  0.327
Carcinogencity:  0.039
Eye Corrosion:  0.003
Eye Irritation:  0.021
Respiratory Toxicity:  0.118

Download Data

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

  Natural Product: NPC325723

Natural Product ID:  NPC325723
Common Name*:   5,6-Dihydro 2'-Deoxythymidine 5'-Phosphate
IUPAC Name:   [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-1,3-diazinan-1-yl)oxolan-2-yl]methyl dihydrogen phosphate
Synonyms:  
Standard InCHIKey:  PGRQANKWVMVANW-UNYLCCJPSA-N
Standard InCHI:  InChI=1S/C10H17N2O8P/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(20-8)4-19-21(16,17)18/h5-8,13H,2-4H2,1H3,(H,11,14,15)(H2,16,17,18)/t5?,6-,7+,8+/m0/s1
SMILES:  CC1CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3228124
PubChem CID:   15276861
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000289] Nucleosides, nucleotides, and analogues
      • [CHEMONTID:0001509] Pyrimidine nucleotides
        • [CHEMONTID:0002148] Pyrimidine deoxyribonucleotides
          • [CHEMONTID:0002151] Pyrimidine deoxyribonucleoside monophosphates
            • [CHEMONTID:0002158] Pyrimidine 2'-deoxyribonucleoside monophosphates

*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
NPT2924 Individual Protein Thymidylate synthase Lactobacillus casei Ki = 150000.0 nM PMID[478031]

☑ 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 NPC325723 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
0.9103 High Similarity NPC325902
0.8427 Intermediate Similarity NPC318166
0.8427 Intermediate Similarity NPC324516
0.8409 Intermediate Similarity NPC327344
0.8272 Intermediate Similarity NPC329077
0.809 Intermediate Similarity NPC324390
0.8 Intermediate Similarity NPC320249
0.8 Intermediate Similarity NPC322594
0.7826 Intermediate Similarity NPC17892
0.7826 Intermediate Similarity NPC36985
0.7742 Intermediate Similarity NPC283698
0.7742 Intermediate Similarity NPC73765
0.7614 Intermediate Similarity NPC112842
0.7614 Intermediate Similarity NPC71339
0.7586 Intermediate Similarity NPC319753
0.7553 Intermediate Similarity NPC317639
0.7391 Intermediate Similarity NPC171116
0.7363 Intermediate Similarity NPC210456
0.7363 Intermediate Similarity NPC163352
0.7303 Intermediate Similarity NPC106780
0.7157 Intermediate Similarity NPC329277
0.7065 Intermediate Similarity NPC89051
0.7065 Intermediate Similarity NPC43246
0.7019 Intermediate Similarity NPC155087
0.7019 Intermediate Similarity NPC149843
0.6907 Remote Similarity NPC329384
0.686 Remote Similarity NPC315806
0.6842 Remote Similarity NPC315063
0.6733 Remote Similarity NPC328914
0.67 Remote Similarity NPC328779
0.6667 Remote Similarity NPC6166
0.6667 Remote Similarity NPC280946
0.6667 Remote Similarity NPC109188
0.6667 Remote Similarity NPC226769
0.66 Remote Similarity NPC120887
0.6436 Remote Similarity NPC90240
0.6306 Remote Similarity NPC478024
0.6224 Remote Similarity NPC328806
0.617 Remote Similarity NPC470783
0.6146 Remote Similarity NPC229249
0.6134 Remote Similarity NPC284651
0.6129 Remote Similarity NPC312315
0.6111 Remote Similarity NPC126186
0.5978 Remote Similarity NPC470782
0.596 Remote Similarity NPC62927
0.596 Remote Similarity NPC190334
0.5854 Remote Similarity NPC293551
0.5755 Remote Similarity NPC313821
0.5714 Remote Similarity NPC214532
0.5714 Remote Similarity NPC76297
0.5714 Remote Similarity NPC470781
0.5714 Remote Similarity NPC196007
0.5696 Remote Similarity NPC224624
0.567 Remote Similarity NPC476302
0.5625 Remote Similarity NPC31756

  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 NPC325723 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
0.7742 Intermediate Similarity NPD9639 Clinical (unspecified phase)
0.7684 Intermediate Similarity NPD5789 Clinical (unspecified phase)
0.7614 Intermediate Similarity NPD280 Approved
0.7582 Intermediate Similarity NPD841 Approved
0.7444 Intermediate Similarity NPD240 Phase 3
0.7273 Intermediate Similarity NPD9556 Approved
0.7253 Intermediate Similarity NPD170 Approved
0.7228 Intermediate Similarity NPD3128 Phase 3
0.7222 Intermediate Similarity NPD238 Clinical (unspecified phase)
0.7222 Intermediate Similarity NPD239 Phase 2
0.7204 Intermediate Similarity NPD755 Phase 3
0.7191 Intermediate Similarity NPD9560 Approved
0.7191 Intermediate Similarity NPD9561 Approved
0.7191 Intermediate Similarity NPD2691 Clinical (unspecified phase)
0.7157 Intermediate Similarity NPD3129 Phase 3
0.7143 Intermediate Similarity NPD9557 Clinical (unspecified phase)
0.7111 Intermediate Similarity NPD9546 Phase 2
0.7111 Intermediate Similarity NPD9559 Phase 1
0.7065 Intermediate Similarity NPD9581 Clinical (unspecified phase)
0.7065 Intermediate Similarity NPD9580 Clinical (unspecified phase)
0.7033 Intermediate Similarity NPD9533 Phase 2
0.6939 Remote Similarity NPD762 Discontinued
0.6889 Remote Similarity NPD9558 Phase 3
0.6882 Remote Similarity NPD9562 Discovery
0.6875 Remote Similarity NPD251 Approved
0.686 Remote Similarity NPD9653 Clinical (unspecified phase)
0.6759 Remote Similarity NPD7914 Suspended
0.6739 Remote Similarity NPD9529 Phase 1
0.6735 Remote Similarity NPD501 Phase 1
0.6733 Remote Similarity NPD1455 Phase 3
0.6733 Remote Similarity NPD1454 Phase 3
0.6667 Remote Similarity NPD1331 Approved
0.6636 Remote Similarity NPD3138 Phase 3
0.6633 Remote Similarity NPD1686 Approved
0.6632 Remote Similarity NPD1760 Approved
0.6598 Remote Similarity NPD9565 Discontinued
0.6577 Remote Similarity NPD3139 Phase 3
0.6552 Remote Similarity NPD9405 Approved
0.6535 Remote Similarity NPD502 Approved
0.6458 Remote Similarity NPD241 Discontinued
0.6415 Remote Similarity NPD6946 Approved
0.6413 Remote Similarity NPD9429 Discontinued
0.6372 Remote Similarity NPD7992 Clinical (unspecified phase)
0.6355 Remote Similarity NPD1385 Discontinued
0.6333 Remote Similarity NPD9407 Approved
0.6226 Remote Similarity NPD1061 Clinical (unspecified phase)
0.6146 Remote Similarity NPD9601 Approved
0.6105 Remote Similarity NPD9573 Phase 2
0.61 Remote Similarity NPD267 Discontinued
0.6095 Remote Similarity NPD223 Clinical (unspecified phase)
0.6061 Remote Similarity NPD301 Discontinued
0.604 Remote Similarity NPD6943 Clinical (unspecified phase)
0.6034 Remote Similarity NPD7756 Clinical (unspecified phase)
0.6019 Remote Similarity NPD2633 Phase 1
0.5982 Remote Similarity NPD3188 Approved
0.596 Remote Similarity NPD9603 Phase 3
0.596 Remote Similarity NPD9602 Phase 3
0.596 Remote Similarity NPD9604 Approved
0.5922 Remote Similarity NPD215 Discontinued
0.5918 Remote Similarity NPD9555 Phase 2
0.59 Remote Similarity NPD9554 Approved
0.59 Remote Similarity NPD9553 Approved
0.5846 Remote Similarity NPD7761 Suspended
0.5833 Remote Similarity NPD9600 Approved
0.5833 Remote Similarity NPD7651 Approved
0.5804 Remote Similarity NPD6693 Phase 3
0.5784 Remote Similarity NPD500 Discontinued
0.5766 Remote Similarity NPD1428 Phase 2
0.5755 Remote Similarity NPD3191 Approved
0.5755 Remote Similarity NPD3189 Approved
0.5755 Remote Similarity NPD3190 Approved
0.5728 Remote Similarity NPD9585 Discontinued
0.5728 Remote Similarity NPD285 Discontinued
0.5714 Remote Similarity NPD9572 Clinical (unspecified phase)
0.5701 Remote Similarity NPD3121 Phase 2
0.5673 Remote Similarity NPD279 Clinical (unspecified phase)
0.566 Remote Similarity NPD514 Clinical (unspecified phase)
0.5632 Remote Similarity NPD9211 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