Structure

Physi-Chem Properties

Molecular Weight:  244.07
Volume:  213.933
LogP:  -1.737
LogD:  -1.56
LogS:  -0.467
# Rotatable Bonds:  2
TPSA:  124.78
# H-Bond Aceptor:  8
# H-Bond Donor:  4
# Rings:  2
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.444
Synthetic Accessibility Score:  3.484
Fsp3:  0.556
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:  -6.015
MDCK Permeability:  0.0003621244977694005
Pgp-inhibitor:  0.001
Pgp-substrate:  0.006
Human Intestinal Absorption (HIA):  0.882
20% Bioavailability (F20%):  0.285
30% Bioavailability (F30%):  0.978

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.439
Plasma Protein Binding (PPB):  13.902139663696289%
Volume Distribution (VD):  0.352
Pgp-substrate:  77.73918914794922%

ADMET: Metabolism

CYP1A2-inhibitor:  0.01
CYP1A2-substrate:  0.105
CYP2C19-inhibitor:  0.024
CYP2C19-substrate:  0.047
CYP2C9-inhibitor:  0.002
CYP2C9-substrate:  0.08
CYP2D6-inhibitor:  0.011
CYP2D6-substrate:  0.084
CYP3A4-inhibitor:  0.004
CYP3A4-substrate:  0.038

ADMET: Excretion

Clearance (CL):  6.501
Half-life (T1/2):  0.867

ADMET: Toxicity

hERG Blockers:  0.008
Human Hepatotoxicity (H-HT):  0.673
Drug-inuced Liver Injury (DILI):  0.983
AMES Toxicity:  0.055
Rat Oral Acute Toxicity:  0.004
Maximum Recommended Daily Dose:  0.004
Skin Sensitization:  0.038
Carcinogencity:  0.042
Eye Corrosion:  0.003
Eye Irritation:  0.019
Respiratory Toxicity:  0.011

Download Data

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

  Natural Product: NPC89051

Natural Product ID:  NPC89051
Common Name*:   Arauridine
IUPAC Name:   1-[(2R,3S,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidine-2,4-dione
Synonyms:   Arauridine
Standard InCHIKey:  DRTQHJPVMGBUCF-CCXZUQQUSA-N
Standard InCHI:  InChI=1S/C9H12N2O6/c12-3-4-6(14)7(15)8(17-4)11-2-1-5(13)10-9(11)16/h1-2,4,6-8,12,14-15H,3H2,(H,10,13,16)/t4-,6-,7+,8-/m1/s1
SMILES:  OC[C@H]1O[C@H]([C@H]([C@@H]1O)O)n1ccc(nc1=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1092065
PubChem CID:   18323
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000289] Nucleosides, nucleotides, and analogues
      • [CHEMONTID:0000480] Pyrimidine nucleosides

*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
NPO19548 Lepisorus contortus Species Polypodiaceae Eukaryota whole plant Gongshan County, Yunnan, China n.a. PMID[21261296]
NPO19548 Lepisorus contortus Species Polypodiaceae Eukaryota n.a. whole plant n.a. PMID[21261296]
NPO19548 Lepisorus contortus Species Polypodiaceae 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
NPT2678 Cell Line NB-4 Homo sapiens IC50 = 69000.0 nM PMID[453561]
NPT116 Cell Line HL-60 Homo sapiens IC50 = 90000.0 nM PMID[453561]
NPT2100 Cell Line KG-1 IC50 = 25000.0 nM PMID[453561]
NPT466 Cell Line U-937 Homo sapiens IC50 > 100000.0 nM PMID[453561]
NPT137 Cell Line L1210 Mus musculus IC50 = 170000.0 nM PMID[453561]
NPT404 Cell Line CCRF-CEM Homo sapiens IC50 > 500000.0 nM PMID[453561]
NPT334 Organism Vaccinia virus Vaccinia virus ID50 = 8.2 10'-4M PMID[453563]
NPT1766 Organism Human herpesvirus 1 strain KOS Human herpesvirus 1 strain KOS ID50 = 4.1 10'-5M PMID[453563]
NPT195 Organism Vesicular stomatitis virus Vesicular stomatitis virus ID50 > 1.0 10'-4M PMID[453563]
NPT195 Organism Vesicular stomatitis virus Vesicular stomatitis virus MIC > 200.0 ug.mL-1 PMID[453564]
NPT334 Organism Vaccinia virus Vaccinia virus MIC > 200.0 ug.mL-1 PMID[453564]
NPT1766 Organism Human herpesvirus 1 strain KOS Human herpesvirus 1 strain KOS MIC = 20.0 ug.mL-1 PMID[453564]
NPT1141 Organism Human herpesvirus 2 Human herpesvirus 2 MIC = 20.0 ug.mL-1 PMID[453564]
NPT27 Others Unspecified MIC = 300.0 ug.mL-1 PMID[453564]
NPT27 Others Unspecified MIC > 400.0 ug.mL-1 PMID[453564]
NPT2 Others Unspecified Ki = 250000.0 nM PMID[453565]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 IC50 > 20000.0 nM PMID[453566]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 IC50 > 19952.62 nM PMID[453566]

☑ 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 NPC89051 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
1.0 High Similarity NPC43246
0.962 High Similarity NPC106780
0.9186 High Similarity NPC36985
0.9186 High Similarity NPC17892
0.9167 High Similarity NPC315063
0.908 High Similarity NPC73765
0.908 High Similarity NPC283698
0.8929 High Similarity NPC210456
0.8929 High Similarity NPC163352
0.8837 High Similarity NPC324390
0.8736 High Similarity NPC322594
0.8736 High Similarity NPC320249
0.8571 High Similarity NPC71339
0.8571 High Similarity NPC112842
0.8395 Intermediate Similarity NPC329077
0.8242 Intermediate Similarity NPC317639
0.8144 Intermediate Similarity NPC329277
0.809 Intermediate Similarity NPC171116
0.8068 Intermediate Similarity NPC62927
0.8068 Intermediate Similarity NPC190334
0.798 Intermediate Similarity NPC149843
0.798 Intermediate Similarity NPC155087
0.7912 Intermediate Similarity NPC327344
0.7742 Intermediate Similarity NPC318166
0.7742 Intermediate Similarity NPC324516
0.7727 Intermediate Similarity NPC229249
0.7647 Intermediate Similarity NPC325902
0.7474 Intermediate Similarity NPC280946
0.7474 Intermediate Similarity NPC6166
0.7474 Intermediate Similarity NPC226769
0.7396 Intermediate Similarity NPC120887
0.7396 Intermediate Similarity NPC90240
0.732 Intermediate Similarity NPC328779
0.7204 Intermediate Similarity NPC328806
0.7172 Intermediate Similarity NPC328914
0.7111 Intermediate Similarity NPC319753
0.7065 Intermediate Similarity NPC325723
0.701 Intermediate Similarity NPC329384
0.6977 Remote Similarity NPC315806
0.693 Remote Similarity NPC284651
0.687 Remote Similarity NPC315058
0.6697 Remote Similarity NPC478024
0.6695 Remote Similarity NPC313962
0.6598 Remote Similarity NPC109188
0.641 Remote Similarity NPC325750
0.6087 Remote Similarity NPC470782
0.6044 Remote Similarity NPC126186
0.5948 Remote Similarity NPC313813
0.5783 Remote Similarity NPC293551
0.5652 Remote Similarity NPC470781
0.5638 Remote Similarity NPC192521
0.5612 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 NPC89051 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
1.0 High Similarity NPD9581 Clinical (unspecified phase)
1.0 High Similarity NPD9580 Clinical (unspecified phase)
0.9383 High Similarity NPD9557 Clinical (unspecified phase)
0.908 High Similarity NPD9639 Clinical (unspecified phase)
0.8889 High Similarity NPD9556 Approved
0.8837 High Similarity NPD9565 Discontinued
0.878 High Similarity NPD9561 Approved
0.878 High Similarity NPD9560 Approved
0.8721 High Similarity NPD755 Phase 3
0.8675 High Similarity NPD9546 Phase 2
0.8659 High Similarity NPD9558 Phase 3
0.8636 High Similarity NPD1686 Approved
0.8571 High Similarity NPD9533 Phase 2
0.8571 High Similarity NPD280 Approved
0.8488 Intermediate Similarity NPD241 Discontinued
0.8462 Intermediate Similarity NPD502 Approved
0.8372 Intermediate Similarity NPD170 Approved
0.8372 Intermediate Similarity NPD240 Phase 3
0.8372 Intermediate Similarity NPD9562 Discovery
0.8235 Intermediate Similarity NPD9529 Phase 1
0.8235 Intermediate Similarity NPD9559 Phase 1
0.8144 Intermediate Similarity NPD3129 Phase 3
0.814 Intermediate Similarity NPD239 Phase 2
0.814 Intermediate Similarity NPD238 Clinical (unspecified phase)
0.8132 Intermediate Similarity NPD501 Phase 1
0.809 Intermediate Similarity NPD841 Approved
0.8068 Intermediate Similarity NPD9604 Approved
0.8068 Intermediate Similarity NPD9602 Phase 3
0.8068 Intermediate Similarity NPD9603 Phase 3
0.8041 Intermediate Similarity NPD3128 Phase 3
0.7957 Intermediate Similarity NPD762 Discontinued
0.7912 Intermediate Similarity NPD251 Approved
0.7835 Intermediate Similarity NPD1061 Clinical (unspecified phase)
0.7727 Intermediate Similarity NPD9601 Approved
0.7717 Intermediate Similarity NPD6943 Clinical (unspecified phase)
0.7717 Intermediate Similarity NPD9585 Discontinued
0.7667 Intermediate Similarity NPD1760 Approved
0.7526 Intermediate Similarity NPD223 Clinical (unspecified phase)
0.7453 Intermediate Similarity NPD3139 Phase 3
0.7426 Intermediate Similarity NPD1385 Discontinued
0.7423 Intermediate Similarity NPD5789 Clinical (unspecified phase)
0.7396 Intermediate Similarity NPD514 Clinical (unspecified phase)
0.7391 Intermediate Similarity NPD9553 Approved
0.7391 Intermediate Similarity NPD301 Discontinued
0.7391 Intermediate Similarity NPD9554 Approved
0.7386 Intermediate Similarity NPD9600 Approved
0.7374 Intermediate Similarity NPD7651 Approved
0.7358 Intermediate Similarity NPD3138 Phase 3
0.7263 Intermediate Similarity NPD279 Clinical (unspecified phase)
0.7234 Intermediate Similarity NPD267 Discontinued
0.7222 Intermediate Similarity NPD9572 Clinical (unspecified phase)
0.7172 Intermediate Similarity NPD1455 Phase 3
0.7172 Intermediate Similarity NPD1454 Phase 3
0.7111 Intermediate Similarity NPD9573 Phase 2
0.7071 Intermediate Similarity NPD192 Phase 2
0.7053 Intermediate Similarity NPD500 Discontinued
0.701 Intermediate Similarity NPD215 Discontinued
0.7009 Intermediate Similarity NPD7914 Suspended
0.6977 Remote Similarity NPD9653 Clinical (unspecified phase)
0.6914 Remote Similarity NPD9503 Approved
0.6914 Remote Similarity NPD9504 Approved
0.6889 Remote Similarity NPD9429 Discontinued
0.6882 Remote Similarity NPD9555 Phase 2
0.6827 Remote Similarity NPD6946 Approved
0.6818 Remote Similarity NPD9407 Approved
0.6731 Remote Similarity NPD2633 Phase 1
0.6667 Remote Similarity NPD1805 Phase 2
0.6667 Remote Similarity NPD1804 Phase 2
0.6604 Remote Similarity NPD1428 Phase 2
0.6598 Remote Similarity NPD1331 Approved
0.6571 Remote Similarity NPD4743 Phase 2
0.6559 Remote Similarity NPD2691 Clinical (unspecified phase)
0.6481 Remote Similarity NPD6693 Phase 3
0.6477 Remote Similarity NPD9405 Approved
0.6421 Remote Similarity NPD205 Approved
0.6408 Remote Similarity NPD3121 Phase 2
0.6404 Remote Similarity NPD7756 Clinical (unspecified phase)
0.6346 Remote Similarity NPD765 Discontinued
0.6316 Remote Similarity NPD6936 Clinical (unspecified phase)
0.6316 Remote Similarity NPD6935 Phase 3
0.63 Remote Similarity NPD285 Discontinued
0.6176 Remote Similarity NPD1706 Clinical (unspecified phase)
0.6172 Remote Similarity NPD7761 Suspended
0.6168 Remote Similarity NPD244 Clinical (unspecified phase)
0.6034 Remote Similarity NPD7992 Clinical (unspecified phase)
0.6 Remote Similarity NPD723 Phase 2
0.5895 Remote Similarity NPD9427 Approved
0.5859 Remote Similarity NPD9640 Clinical (unspecified phase)
0.5847 Remote Similarity NPD6918 Phase 1
0.581 Remote Similarity NPD6948 Phase 3
0.5789 Remote Similarity NPD9372 Phase 2
0.5755 Remote Similarity NPD2621 Clinical (unspecified phase)
0.5747 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