Structure

Physi-Chem Properties

Molecular Weight:  561.88
Volume:  371.81
LogP:  -2.7
LogD:  -1.303
LogS:  -0.268
# Rotatable Bonds:  8
TPSA:  254.89
# H-Bond Aceptor:  17
# H-Bond Donor:  4
# Rings:  2
# Heavy Atoms:  21

MedChem Properties

QED Drug-Likeness Score:  0.27
Synthetic Accessibility Score:  5.906
Fsp3:  0.556
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.426
MDCK Permeability:  0.00014986087626311928
Pgp-inhibitor:  0.0
Pgp-substrate:  0.005
Human Intestinal Absorption (HIA):  0.979
20% Bioavailability (F20%):  0.998
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.439
Plasma Protein Binding (PPB):  29.392641067504883%
Volume Distribution (VD):  0.328
Pgp-substrate:  62.739933013916016%

ADMET: Metabolism

CYP1A2-inhibitor:  0.001
CYP1A2-substrate:  0.04
CYP2C19-inhibitor:  0.043
CYP2C19-substrate:  0.02
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.112
CYP2D6-inhibitor:  0.046
CYP2D6-substrate:  0.047
CYP3A4-inhibitor:  0.001
CYP3A4-substrate:  0.001

ADMET: Excretion

Clearance (CL):  1.592
Half-life (T1/2):  0.89

ADMET: Toxicity

hERG Blockers:  0.002
Human Hepatotoxicity (H-HT):  0.149
Drug-inuced Liver Injury (DILI):  0.977
AMES Toxicity:  0.026
Rat Oral Acute Toxicity:  0.001
Maximum Recommended Daily Dose:  0.934
Skin Sensitization:  0.529
Carcinogencity:  0.302
Eye Corrosion:  0.003
Eye Irritation:  0.021
Respiratory Toxicity:  0.52

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General Info & Identifiers & Properties  
Structure MOL file  
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Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC317639

Natural Product ID:  NPC317639
Common Name*:   5-Bromo-Utp
IUPAC Name:   [[(2R,3S,4R,5R)-5-(5-bromo-2,4-dioxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy-hydroxyphosphoryl] phosphono hydrogen phosphate
Synonyms:   5-bromo-UTP
Standard InCHIKey:  IWFHOSULCAJGRM-UAKXSSHOSA-N
Standard InCHI:  InChI=1S/C9H14BrN2O15P3/c10-3-1-12(9(16)11-7(3)15)8-6(14)5(13)4(25-8)2-24-29(20,21)27-30(22,23)26-28(17,18)19/h1,4-6,8,13-14H,2H2,(H,20,21)(H,22,23)(H,11,15,16)(H2,17,18,19)/t4-,5-,6-,8-/m1/s1
SMILES:  O[C@@H]1[C@@H](COP(=O)(OP(=O)(OP(=O)(O)O)O)O)O[C@H]([C@@H]1O)n1cc(Br)c(nc1=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL384527
PubChem CID:   9872620
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000289] Nucleosides, nucleotides, and analogues
      • [CHEMONTID:0001509] Pyrimidine nucleotides
        • [CHEMONTID:0002147] Pyrimidine ribonucleotides
          • [CHEMONTID:0001622] Pyrimidine ribonucleoside triphosphates

*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. urine n.a. PMID[20708442]
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. 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
NPT3826 Individual Protein Purinergic receptor P2Y2 Homo sapiens EC50 = 347.0 nM PMID[575428]
NPT3827 Individual Protein Pyrimidinergic receptor P2Y4 Homo sapiens EC50 = 3460.0 nM PMID[575428]
NPT1391 Individual Protein Pyrimidinergic receptor P2Y6 Homo sapiens EC50 = 291.0 nM PMID[575428]
NPT3826 Individual Protein Purinergic receptor P2Y2 Homo sapiens EC50 = 750.0 nM PMID[575429]
NPT3826 Individual Protein Purinergic receptor P2Y2 Homo sapiens EC50 = 2060.0 nM PMID[575430]
NPT3827 Individual Protein Pyrimidinergic receptor P2Y4 Homo sapiens EC50 = 10000.0 nM PMID[575430]
NPT1391 Individual Protein Pyrimidinergic receptor P2Y6 Homo sapiens EC50 = 800.0 nM PMID[575430]
NPT3826 Individual Protein Purinergic receptor P2Y2 Homo sapiens EC50 = 220.0 nM PMID[575431]

☑ 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 NPC317639 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
0.9121 High Similarity NPC73765
0.9121 High Similarity NPC283698
0.9011 High Similarity NPC36985
0.9011 High Similarity NPC17892
0.8791 High Similarity NPC320249
0.8791 High Similarity NPC322594
0.8681 High Similarity NPC324390
0.8602 High Similarity NPC324516
0.8602 High Similarity NPC318166
0.8587 High Similarity NPC327344
0.8242 Intermediate Similarity NPC89051
0.8242 Intermediate Similarity NPC43246
0.8218 Intermediate Similarity NPC329277
0.8152 Intermediate Similarity NPC163352
0.8152 Intermediate Similarity NPC210456
0.8058 Intermediate Similarity NPC149843
0.8058 Intermediate Similarity NPC155087
0.7912 Intermediate Similarity NPC106780
0.7826 Intermediate Similarity NPC71339
0.7826 Intermediate Similarity NPC112842
0.7604 Intermediate Similarity NPC315063
0.7553 Intermediate Similarity NPC325723
0.75 Intermediate Similarity NPC120887
0.7444 Intermediate Similarity NPC329077
0.7426 Intermediate Similarity NPC328779
0.7423 Intermediate Similarity NPC171116
0.74 Intermediate Similarity NPC226769
0.74 Intermediate Similarity NPC280946
0.74 Intermediate Similarity NPC6166
0.7282 Intermediate Similarity NPC328914
0.7157 Intermediate Similarity NPC90240
0.7129 Intermediate Similarity NPC329384
0.7034 Intermediate Similarity NPC284651
0.6809 Remote Similarity NPC325902
0.67 Remote Similarity NPC190334
0.67 Remote Similarity NPC62927
0.6634 Remote Similarity NPC328806
0.64 Remote Similarity NPC229249
0.6383 Remote Similarity NPC315806
0.6364 Remote Similarity NPC319753
0.6095 Remote Similarity NPC109188
0.6032 Remote Similarity NPC315058
0.6 Remote Similarity NPC325750
0.5966 Remote Similarity NPC478024
0.5891 Remote Similarity NPC313962

  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 NPC317639 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
0.9121 High Similarity NPD9639 Clinical (unspecified phase)
0.8736 High Similarity NPD9546 Phase 2
0.8242 Intermediate Similarity NPD9581 Clinical (unspecified phase)
0.8242 Intermediate Similarity NPD9580 Clinical (unspecified phase)
0.8218 Intermediate Similarity NPD3129 Phase 3
0.8119 Intermediate Similarity NPD3128 Phase 3
0.809 Intermediate Similarity NPD9556 Approved
0.8061 Intermediate Similarity NPD5789 Clinical (unspecified phase)
0.8 Intermediate Similarity NPD9560 Approved
0.8 Intermediate Similarity NPD9561 Approved
0.7979 Intermediate Similarity NPD755 Phase 3
0.7959 Intermediate Similarity NPD502 Approved
0.7889 Intermediate Similarity NPD9558 Phase 3
0.7826 Intermediate Similarity NPD280 Approved
0.7826 Intermediate Similarity NPD9533 Phase 2
0.7766 Intermediate Similarity NPD241 Discontinued
0.7742 Intermediate Similarity NPD9557 Clinical (unspecified phase)
0.766 Intermediate Similarity NPD240 Phase 3
0.766 Intermediate Similarity NPD170 Approved
0.766 Intermediate Similarity NPD9562 Discovery
0.7653 Intermediate Similarity NPD501 Phase 1
0.7593 Intermediate Similarity NPD7914 Suspended
0.7545 Intermediate Similarity NPD3139 Phase 3
0.7527 Intermediate Similarity NPD9559 Phase 1
0.7527 Intermediate Similarity NPD9529 Phase 1
0.7455 Intermediate Similarity NPD3138 Phase 3
0.7447 Intermediate Similarity NPD239 Phase 2
0.7447 Intermediate Similarity NPD238 Clinical (unspecified phase)
0.7423 Intermediate Similarity NPD841 Approved
0.7374 Intermediate Similarity NPD1686 Approved
0.7347 Intermediate Similarity NPD9565 Discontinued
0.7282 Intermediate Similarity NPD1454 Phase 3
0.7282 Intermediate Similarity NPD1455 Phase 3
0.7273 Intermediate Similarity NPD251 Approved
0.7041 Intermediate Similarity NPD1760 Approved
0.6952 Remote Similarity NPD223 Clinical (unspecified phase)
0.6916 Remote Similarity NPD1061 Clinical (unspecified phase)
0.6881 Remote Similarity NPD1385 Discontinued
0.6789 Remote Similarity NPD6946 Approved
0.67 Remote Similarity NPD9603 Phase 3
0.67 Remote Similarity NPD9604 Approved
0.67 Remote Similarity NPD9602 Phase 3
0.6667 Remote Similarity NPD500 Discontinued
0.6667 Remote Similarity NPD762 Discontinued
0.6667 Remote Similarity NPD7756 Clinical (unspecified phase)
0.6581 Remote Similarity NPD7992 Clinical (unspecified phase)
0.6531 Remote Similarity NPD9573 Phase 2
0.6442 Remote Similarity NPD6943 Clinical (unspecified phase)
0.6442 Remote Similarity NPD9585 Discontinued
0.64 Remote Similarity NPD9601 Approved
0.6383 Remote Similarity NPD9653 Clinical (unspecified phase)
0.6337 Remote Similarity NPD9555 Phase 2
0.6327 Remote Similarity NPD9429 Discontinued
0.6292 Remote Similarity NPD9503 Approved
0.6292 Remote Similarity NPD9504 Approved
0.6288 Remote Similarity NPD7761 Suspended
0.625 Remote Similarity NPD9407 Approved
0.6226 Remote Similarity NPD279 Clinical (unspecified phase)
0.6216 Remote Similarity NPD7651 Approved
0.6204 Remote Similarity NPD514 Clinical (unspecified phase)
0.6154 Remote Similarity NPD9554 Approved
0.6154 Remote Similarity NPD301 Discontinued
0.6154 Remote Similarity NPD9553 Approved
0.6121 Remote Similarity NPD284 Phase 1
0.61 Remote Similarity NPD9600 Approved
0.6095 Remote Similarity NPD1331 Approved
0.6038 Remote Similarity NPD267 Discontinued
0.6036 Remote Similarity NPD765 Discontinued
0.598 Remote Similarity NPD9572 Clinical (unspecified phase)
0.5946 Remote Similarity NPD192 Phase 2
0.5938 Remote Similarity NPD9405 Approved
0.5882 Remote Similarity NPD2691 Clinical (unspecified phase)
0.5872 Remote Similarity NPD215 Discontinued
0.5833 Remote Similarity NPD285 Discontinued
0.569 Remote Similarity NPD2633 Phase 1
0.569 Remote Similarity NPD4743 Phase 2
0.5676 Remote Similarity NPD6948 Phase 3
0.5667 Remote Similarity NPD1805 Phase 2
0.5667 Remote Similarity NPD1804 Phase 2
0.5619 Remote Similarity NPD205 Approved

  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