Structure

Physi-Chem Properties

Molecular Weight:  614.15
Volume:  520.082
LogP:  -3.389
LogD:  -1.933
LogS:  0.298
# Rotatable Bonds:  12
TPSA:  320.48
# H-Bond Aceptor:  20
# H-Bond Donor:  10
# Rings:  3
# Heavy Atoms:  21

MedChem Properties

QED Drug-Likeness Score:  0.104
Synthetic Accessibility Score:  5.746
Fsp3:  0.7
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.928
MDCK Permeability:  0.00030848104506731033
Pgp-inhibitor:  0.0
Pgp-substrate:  0.98
Human Intestinal Absorption (HIA):  0.994
20% Bioavailability (F20%):  1.0
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.405
Plasma Protein Binding (PPB):  17.60649871826172%
Volume Distribution (VD):  0.24
Pgp-substrate:  75.28865814208984%

ADMET: Metabolism

CYP1A2-inhibitor:  0.0
CYP1A2-substrate:  0.02
CYP2C19-inhibitor:  0.027
CYP2C19-substrate:  0.028
CYP2C9-inhibitor:  0.003
CYP2C9-substrate:  0.02
CYP2D6-inhibitor:  0.015
CYP2D6-substrate:  0.042
CYP3A4-inhibitor:  0.003
CYP3A4-substrate:  0.001

ADMET: Excretion

Clearance (CL):  1.243
Half-life (T1/2):  0.845

ADMET: Toxicity

hERG Blockers:  0.021
Human Hepatotoxicity (H-HT):  0.655
Drug-inuced Liver Injury (DILI):  0.981
AMES Toxicity:  0.028
Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.023
Skin Sensitization:  0.139
Carcinogencity:  0.022
Eye Corrosion:  0.003
Eye Irritation:  0.023
Respiratory Toxicity:  0.02

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Similar NPs/Drugs  

  Natural Product: NPC318142

Natural Product ID:  NPC318142
Common Name*:   (2R,4S,5R,6R)-5-Acetamido-2-[[(2R,3S,4R,5R)-5-(4-Amino-2-Oxopyrimidin-1-Yl)-3,4-Dihydroxyoxolan-2-Yl]Methoxy-Hydroxyphosphoryl]Oxy-4-Hydroxy-6-[(1R,2R)-1,2,3-Trihydroxypropyl]Oxane-2-Carboxylic Acid
IUPAC Name:   (2R,4S,5R,6R)-5-acetamido-2-[[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-4-hydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]oxane-2-carboxylic acid
Synonyms:  
Standard InCHIKey:  TXCIAUNLDRJGJZ-BILDWYJOSA-N
Standard InCHI:  InChI=1S/C20H31N4O16P/c1-7(26)22-12-8(27)4-20(18(32)33,39-16(12)13(29)9(28)5-25)40-41(35,36)37-6-10-14(30)15(31)17(38-10)24-3-2-11(21)23-19(24)34/h2-3,8-10,12-17,25,27-31H,4-6H2,1H3,(H,22,26)(H,32,33)(H,35,36)(H2,21,23,34)/t8-,9+,10+,12+,13+,14+,15+,16+,17+,20+/m0/s1
SMILES:  CC(=O)NC1C(CC(OC1C(C(CO)O)O)(C(=O)O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=NC3=O)N)O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1234647
PubChem CID:   448209
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000289] Nucleosides, nucleotides, and analogues
      • [CHEMONTID:0001509] Pyrimidine nucleotides
        • [CHEMONTID:0001296] Pyrimidine nucleotide sugars

*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
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. DOI[10.1172/JCI16309]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. DOI[10.1371/journal.pone.0115359]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[10557354]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[11034610]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[11419736]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[11530998]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[1175644]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[12391014]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[12812989]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[12840027]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[12878451]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[15084647]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[1521032]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[15230696]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[15314235]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[16112079]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[16770722]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[1687010]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[17116739]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[17190852]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[17875433]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[18311922]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[18544912]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[18799520]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[19425150]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[19961175]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[20506249]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[20601097]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. faeces n.a. PMID[20708442]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. bile n.a. PMID[20708442]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. urine n.a. PMID[20708442]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[20876113]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[21798258]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[2268561]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[22711758]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[23315938]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[23717534]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[23752203]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[23810710]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[23811455]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[23868375]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[23919613]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[24101735]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[24399466]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[24494566]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[24558969]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[24816727]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[25114169]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[25181601]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[25293588]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[25644343]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[26236990]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[27471436]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[3179836]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[347637]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[4696527]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[5432584]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[6121420]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[6780563]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[8600370]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[8987136]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[9192820]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. PMID[9800648]
NPO20338 Mus musculus Species Muridae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO20338 Mus musculus Species Muridae 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
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 > 50000.0 nM PMID[567365]
NPT2 Others Unspecified IC50 = 35000.0 nM PMID[567365]
NPT6724 Individual Protein Beta-galactoside alpha-2,6-sialyltransferase 1 Homo sapiens Km = 37200.0 nM PMID[567366]

☑ 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 NPC318142 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
0.7405 Intermediate Similarity NPC313813
0.7353 Intermediate Similarity NPC284651
0.7317 Intermediate Similarity NPC328914
0.7213 Intermediate Similarity NPC90240
0.7154 Intermediate Similarity NPC328779
0.7131 Intermediate Similarity NPC226769
0.7131 Intermediate Similarity NPC6166
0.7131 Intermediate Similarity NPC280946
0.7073 Intermediate Similarity NPC120887
0.6911 Remote Similarity NPC329384
0.6742 Remote Similarity NPC155087
0.6742 Remote Similarity NPC149843
0.6721 Remote Similarity NPC292345
0.6557 Remote Similarity NPC62927
0.6557 Remote Similarity NPC190334
0.6538 Remote Similarity NPC42320
0.6538 Remote Similarity NPC188453
0.646 Remote Similarity NPC316244
0.6434 Remote Similarity NPC325750
0.6311 Remote Similarity NPC229249
0.6294 Remote Similarity NPC245534
0.6222 Remote Similarity NPC329277
0.6214 Remote Similarity NPC259586
0.617 Remote Similarity NPC222481
0.617 Remote Similarity NPC470621
0.6124 Remote Similarity NPC17892
0.6124 Remote Similarity NPC36985
0.6111 Remote Similarity NPC328806
0.6077 Remote Similarity NPC73765
0.6077 Remote Similarity NPC283698
0.6024 Remote Similarity NPC317377
0.6024 Remote Similarity NPC321485
0.6024 Remote Similarity NPC319334
0.6024 Remote Similarity NPC327517
0.6024 Remote Similarity NPC322372
0.6 Remote Similarity NPC313962
0.5912 Remote Similarity NPC322449
0.5912 Remote Similarity NPC189854
0.5912 Remote Similarity NPC62845
0.5912 Remote Similarity NPC166242
0.5912 Remote Similarity NPC92874
0.5906 Remote Similarity NPC315058
0.5891 Remote Similarity NPC324390
0.587 Remote Similarity NPC325900
0.587 Remote Similarity NPC10897
0.5846 Remote Similarity NPC320249
0.5846 Remote Similarity NPC322594
0.5839 Remote Similarity NPC314413
0.5839 Remote Similarity NPC239705
0.5839 Remote Similarity NPC314398
0.5755 Remote Similarity NPC475918
0.5714 Remote Similarity NPC477398
0.5705 Remote Similarity NPC94319
0.5682 Remote Similarity NPC270005
0.5682 Remote Similarity NPC208537
0.5644 Remote Similarity NPC477519
0.5629 Remote Similarity NPC470650
0.5629 Remote Similarity NPC470654
0.5629 Remote Similarity NPC470653

  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 NPC318142 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
0.7724 Intermediate Similarity NPD6946 Approved
0.7481 Intermediate Similarity NPD6936 Clinical (unspecified phase)
0.7481 Intermediate Similarity NPD6935 Phase 3
0.7317 Intermediate Similarity NPD1454 Phase 3
0.7317 Intermediate Similarity NPD1455 Phase 3
0.72 Intermediate Similarity NPD7651 Approved
0.7154 Intermediate Similarity NPD1804 Phase 2
0.7154 Intermediate Similarity NPD1805 Phase 2
0.7109 Intermediate Similarity NPD1428 Phase 2
0.7087 Intermediate Similarity NPD4743 Phase 2
0.7037 Intermediate Similarity NPD6918 Phase 1
0.694 Remote Similarity NPD3138 Phase 3
0.6889 Remote Similarity NPD3139 Phase 3
0.6855 Remote Similarity NPD6948 Phase 3
0.6748 Remote Similarity NPD6943 Clinical (unspecified phase)
0.6721 Remote Similarity NPD618 Clinical (unspecified phase)
0.6692 Remote Similarity NPD6941 Approved
0.6617 Remote Similarity NPD6693 Phase 3
0.6613 Remote Similarity NPD9585 Discontinued
0.6565 Remote Similarity NPD3161 Clinical (unspecified phase)
0.6557 Remote Similarity NPD9604 Approved
0.6557 Remote Similarity NPD9603 Phase 3
0.6557 Remote Similarity NPD9602 Phase 3
0.6458 Remote Similarity NPD4816 Clinical (unspecified phase)
0.6434 Remote Similarity NPD3121 Phase 2
0.6429 Remote Similarity NPD7756 Clinical (unspecified phase)
0.6316 Remote Similarity NPD2633 Phase 1
0.6311 Remote Similarity NPD9601 Approved
0.6269 Remote Similarity NPD3128 Phase 3
0.6222 Remote Similarity NPD3129 Phase 3
0.6154 Remote Similarity NPD2621 Clinical (unspecified phase)
0.6154 Remote Similarity NPD514 Clinical (unspecified phase)
0.6142 Remote Similarity NPD267 Discontinued
0.6124 Remote Similarity NPD1706 Clinical (unspecified phase)
0.6111 Remote Similarity NPD301 Discontinued
0.6111 Remote Similarity NPD9554 Approved
0.6111 Remote Similarity NPD9553 Approved
0.6077 Remote Similarity NPD9639 Clinical (unspecified phase)
0.6066 Remote Similarity NPD9600 Approved
0.6061 Remote Similarity NPD5789 Clinical (unspecified phase)
0.6 Remote Similarity NPD215 Discontinued
0.5969 Remote Similarity NPD285 Discontinued
0.5968 Remote Similarity NPD9572 Clinical (unspecified phase)
0.5944 Remote Similarity NPD869 Approved
0.5923 Remote Similarity NPD1686 Approved
0.5891 Remote Similarity NPD3716 Discontinued
0.5887 Remote Similarity NPD9573 Phase 2
0.5882 Remote Similarity NPD7140 Approved
0.5882 Remote Similarity NPD7141 Clinical (unspecified phase)
0.5882 Remote Similarity NPD7139 Approved
0.5878 Remote Similarity NPD1446 Phase 3
0.5878 Remote Similarity NPD1447 Phase 3
0.587 Remote Similarity NPD1385 Discontinued
0.5857 Remote Similarity NPD284 Phase 1
0.5845 Remote Similarity NPD7914 Suspended
0.5839 Remote Similarity NPD8045 Clinical (unspecified phase)
0.5778 Remote Similarity NPD2255 Approved
0.5772 Remote Similarity NPD9403 Discontinued
0.5772 Remote Similarity NPD9427 Approved
0.576 Remote Similarity NPD2691 Clinical (unspecified phase)
0.5748 Remote Similarity NPD9555 Phase 2
0.5746 Remote Similarity NPD6428 Approved
0.5723 Remote Similarity NPD7761 Suspended
0.5714 Remote Similarity NPD8394 Approved
0.5714 Remote Similarity NPD883 Phase 2
0.5714 Remote Similarity NPD882 Phase 2
0.5705 Remote Similarity NPD4828 Approved
0.5705 Remote Similarity NPD4827 Approved
0.5705 Remote Similarity NPD4826 Approved
0.5704 Remote Similarity NPD192 Phase 2
0.5703 Remote Similarity NPD619 Phase 3
0.5664 Remote Similarity NPD2690 Discontinued
0.5659 Remote Similarity NPD1760 Approved
0.5652 Remote Similarity NPD244 Clinical (unspecified phase)
0.5652 Remote Similarity NPD1061 Clinical (unspecified phase)
0.5628 Remote Similarity NPD6237 Clinical (unspecified phase)
0.5603 Remote Similarity NPD8307 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