Structure

Physi-Chem Properties

Molecular Weight:  284.1
Volume:  263.184
LogP:  -0.625
LogD:  -0.344
LogS:  -1.206
# Rotatable Bonds:  4
TPSA:  110.62
# H-Bond Aceptor:  8
# H-Bond Donor:  2
# Rings:  2
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.693
Synthetic Accessibility Score:  3.434
Fsp3:  0.583
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:  -5.661
MDCK Permeability:  0.00024293144815601408
Pgp-inhibitor:  0.003
Pgp-substrate:  0.111
Human Intestinal Absorption (HIA):  0.124
20% Bioavailability (F20%):  0.091
30% Bioavailability (F30%):  0.603

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.328
Plasma Protein Binding (PPB):  13.110405921936035%
Volume Distribution (VD):  0.589
Pgp-substrate:  78.7946548461914%

ADMET: Metabolism

CYP1A2-inhibitor:  0.017
CYP1A2-substrate:  0.087
CYP2C19-inhibitor:  0.024
CYP2C19-substrate:  0.061
CYP2C9-inhibitor:  0.004
CYP2C9-substrate:  0.134
CYP2D6-inhibitor:  0.039
CYP2D6-substrate:  0.104
CYP3A4-inhibitor:  0.013
CYP3A4-substrate:  0.392

ADMET: Excretion

Clearance (CL):  8.063
Half-life (T1/2):  0.921

ADMET: Toxicity

hERG Blockers:  0.009
Human Hepatotoxicity (H-HT):  0.977
Drug-inuced Liver Injury (DILI):  0.987
AMES Toxicity:  0.305
Rat Oral Acute Toxicity:  0.007
Maximum Recommended Daily Dose:  0.051
Skin Sensitization:  0.093
Carcinogencity:  0.447
Eye Corrosion:  0.003
Eye Irritation:  0.018
Respiratory Toxicity:  0.005

Download Data

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

  Natural Product: NPC171116

Natural Product ID:  NPC171116
Common Name*:   3'-O-Acetyl-2'-Deoxythymidine
IUPAC Name:   [(2R,3S,5R)-2-(hydroxymethyl)-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-3-yl] acetate
Synonyms:  
Standard InCHIKey:  IRFKBRPHBYCMQU-IVZWLZJFSA-N
Standard InCHI:  InChI=1S/C12H16N2O6/c1-6-4-14(12(18)13-11(6)17)10-3-8(19-7(2)16)9(5-15)20-10/h4,8-10,15H,3,5H2,1-2H3,(H,13,17,18)/t8-,9+,10+/m0/s1
SMILES:  OC[C@H]1O[C@H](C[C@@H]1OC(=O)C)n1cc(C)c(nc1=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL266234
PubChem CID:   464365
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000289] Nucleosides, nucleotides, and analogues
      • [CHEMONTID:0000480] Pyrimidine nucleosides
        • [CHEMONTID:0002180] Pyrimidine 2'-deoxyribonucleosides

*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
NPO19812 Pimelea simplex Species Thymelaeaceae Eukaryota n.a. n.a. n.a. PMID[21049973]
NPO12352 Magnolia baillonii Species Magnoliaceae Eukaryota n.a. n.a. n.a. PMID[3437284]
NPO19551 Cocculus pendulus Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19812 Pimelea simplex Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19551 Cocculus pendulus Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19812 Pimelea simplex Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19611 Ipomoea tuberosa Species Convolvulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19812 Pimelea simplex Species Thymelaeaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13189 Carex folliculata Species Cyperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16902 Dendroctonus brevicomis Species Curculionidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11741 Glycosmis parviflora Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18651 Piper lolot Species Piperaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18223 Dictyostelium brefeldianum Species n.a. Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19146 Cosmos bipinnatus Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19551 Cocculus pendulus Species Menispermaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14131 Phyllanthus maderaspatensis Species Phyllanthaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19681 Hypoxis filiformis Species Hypoxidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18898 Madhuca utilis Species Sapotaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17984 Aplysia angasi Species Aplysiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10921 Cercospora ligustri Species Mycosphaerellaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12352 Magnolia baillonii Species Magnoliaceae 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
NPT1452 Cell Line C8166 Homo sapiens ED50 > 200.0 uM PMID[448804]
NPT1452 Cell Line C8166 Homo sapiens TD50 > 200.0 uM PMID[448804]
NPT27 Others Unspecified T1/2 = 135.0 hr PMID[448803]
NPT907 Individual Protein Ribonuclease pancreatic Homo sapiens Inhibition = 38.0 % PMID[448805]
NPT907 Individual Protein Ribonuclease pancreatic Homo sapiens IC50 = 197000.0 nM PMID[448805]
NPT907 Individual Protein Ribonuclease pancreatic Homo sapiens Ki = 42000.0 nM PMID[448805]
NPT2 Others Unspecified Ki = 58000.0 nM PMID[448806]

☑ 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 NPC171116 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
0.939 High Similarity NPC112842
0.939 High Similarity NPC71339
0.9059 High Similarity NPC210456
0.9059 High Similarity NPC163352
0.8667 High Similarity NPC318166
0.8667 High Similarity NPC324516
0.8652 High Similarity NPC327344
0.8372 Intermediate Similarity NPC106780
0.809 Intermediate Similarity NPC43246
0.809 Intermediate Similarity NPC89051
0.8 Intermediate Similarity NPC325902
0.7742 Intermediate Similarity NPC324390
0.766 Intermediate Similarity NPC322594
0.766 Intermediate Similarity NPC320249
0.75 Intermediate Similarity NPC17892
0.75 Intermediate Similarity NPC36985
0.7471 Intermediate Similarity NPC329077
0.7447 Intermediate Similarity NPC315063
0.7423 Intermediate Similarity NPC317639
0.7423 Intermediate Similarity NPC283698
0.7423 Intermediate Similarity NPC73765
0.7391 Intermediate Similarity NPC325723
0.734 Intermediate Similarity NPC328806
0.7065 Intermediate Similarity NPC319753
0.6916 Remote Similarity NPC155087
0.6916 Remote Similarity NPC149843
0.6887 Remote Similarity NPC329277
0.681 Remote Similarity NPC325750
0.6737 Remote Similarity NPC229249
0.6735 Remote Similarity NPC109188
0.6667 Remote Similarity NPC478024
0.6531 Remote Similarity NPC190334
0.6531 Remote Similarity NPC62927
0.6471 Remote Similarity NPC284651
0.6374 Remote Similarity NPC315806
0.6311 Remote Similarity NPC329384
0.6281 Remote Similarity NPC315058
0.6168 Remote Similarity NPC328914
0.6132 Remote Similarity NPC328779
0.6129 Remote Similarity NPC313962
0.6095 Remote Similarity NPC226769
0.6095 Remote Similarity NPC280946
0.6095 Remote Similarity NPC6166
0.6042 Remote Similarity NPC316123
0.6038 Remote Similarity NPC90240
0.6038 Remote Similarity NPC120887
0.5691 Remote Similarity NPC245534
0.5684 Remote Similarity NPC126186
0.56 Remote Similarity NPC470783

  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 NPC171116 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
0.939 High Similarity NPD280 Approved
0.9167 High Similarity NPD240 Phase 3
0.907 High Similarity NPD841 Approved
0.8929 High Similarity NPD238 Clinical (unspecified phase)
0.8929 High Similarity NPD239 Phase 2
0.8721 High Similarity NPD170 Approved
0.8636 High Similarity NPD755 Phase 3
0.8571 High Similarity NPD9556 Approved
0.8471 Intermediate Similarity NPD9561 Approved
0.8471 Intermediate Similarity NPD9560 Approved
0.8444 Intermediate Similarity NPD251 Approved
0.8372 Intermediate Similarity NPD9546 Phase 2
0.8276 Intermediate Similarity NPD9533 Phase 2
0.8261 Intermediate Similarity NPD501 Phase 1
0.8182 Intermediate Similarity NPD9557 Clinical (unspecified phase)
0.8161 Intermediate Similarity NPD9559 Phase 1
0.8152 Intermediate Similarity NPD1686 Approved
0.814 Intermediate Similarity NPD9558 Phase 3
0.809 Intermediate Similarity NPD9580 Clinical (unspecified phase)
0.809 Intermediate Similarity NPD9581 Clinical (unspecified phase)
0.809 Intermediate Similarity NPD9562 Discovery
0.8 Intermediate Similarity NPD502 Approved
0.7955 Intermediate Similarity NPD9529 Phase 1
0.79 Intermediate Similarity NPD1385 Discontinued
0.7609 Intermediate Similarity NPD1760 Approved
0.7609 Intermediate Similarity NPD241 Discontinued
0.7553 Intermediate Similarity NPD9565 Discontinued
0.7551 Intermediate Similarity NPD5789 Clinical (unspecified phase)
0.7423 Intermediate Similarity NPD9639 Clinical (unspecified phase)
0.7347 Intermediate Similarity NPD762 Discontinued
0.7087 Intermediate Similarity NPD1061 Clinical (unspecified phase)
0.701 Intermediate Similarity NPD500 Discontinued
0.697 Remote Similarity NPD1706 Clinical (unspecified phase)
0.6887 Remote Similarity NPD3129 Phase 3
0.6882 Remote Similarity NPD9573 Phase 2
0.6796 Remote Similarity NPD223 Clinical (unspecified phase)
0.6792 Remote Similarity NPD3128 Phase 3
0.6768 Remote Similarity NPD285 Discontinued
0.6737 Remote Similarity NPD9601 Approved
0.6737 Remote Similarity NPD205 Approved
0.6735 Remote Similarity NPD1331 Approved
0.6729 Remote Similarity NPD1428 Phase 2
0.6702 Remote Similarity NPD2691 Clinical (unspecified phase)
0.6699 Remote Similarity NPD3121 Phase 2
0.6699 Remote Similarity NPD192 Phase 2
0.6667 Remote Similarity NPD7756 Clinical (unspecified phase)
0.6667 Remote Similarity NPD9555 Phase 2
0.6667 Remote Similarity NPD267 Discontinued
0.6667 Remote Similarity NPD9503 Approved
0.6667 Remote Similarity NPD7914 Suspended
0.6667 Remote Similarity NPD9504 Approved
0.66 Remote Similarity NPD6943 Clinical (unspecified phase)
0.6579 Remote Similarity NPD7992 Clinical (unspecified phase)
0.6542 Remote Similarity NPD2633 Phase 1
0.6531 Remote Similarity NPD9604 Approved
0.6531 Remote Similarity NPD9603 Phase 3
0.6531 Remote Similarity NPD9602 Phase 3
0.6509 Remote Similarity NPD7651 Approved
0.6486 Remote Similarity NPD1805 Phase 2
0.6486 Remote Similarity NPD1804 Phase 2
0.6476 Remote Similarity NPD765 Discontinued
0.6465 Remote Similarity NPD301 Discontinued
0.6465 Remote Similarity NPD9553 Approved
0.6465 Remote Similarity NPD9554 Approved
0.6421 Remote Similarity NPD9600 Approved
0.6389 Remote Similarity NPD4743 Phase 2
0.6374 Remote Similarity NPD9653 Clinical (unspecified phase)
0.6373 Remote Similarity NPD279 Clinical (unspecified phase)
0.6348 Remote Similarity NPD3139 Phase 3
0.6311 Remote Similarity NPD215 Discontinued
0.6306 Remote Similarity NPD6693 Phase 3
0.63 Remote Similarity NPD723 Phase 2
0.6289 Remote Similarity NPD9572 Clinical (unspecified phase)
0.6275 Remote Similarity NPD9585 Discontinued
0.6264 Remote Similarity NPD9405 Approved
0.6261 Remote Similarity NPD3138 Phase 3
0.619 Remote Similarity NPD514 Clinical (unspecified phase)
0.6168 Remote Similarity NPD1454 Phase 3
0.6168 Remote Similarity NPD1455 Phase 3
0.6154 Remote Similarity NPD6936 Clinical (unspecified phase)
0.6154 Remote Similarity NPD6935 Phase 3
0.6146 Remote Similarity NPD9429 Discontinued
0.6102 Remote Similarity NPD6918 Phase 1
0.6064 Remote Similarity NPD9407 Approved
0.5893 Remote Similarity NPD6946 Approved
0.5888 Remote Similarity NPD2621 Clinical (unspecified phase)
0.5672 Remote Similarity NPD7761 Suspended
0.5644 Remote Similarity NPD882 Phase 2
0.5644 Remote Similarity NPD883 Phase 2

  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