Structure

Physi-Chem Properties

Molecular Weight:  202.12
Volume:  211.404
LogP:  3.073
LogD:  2.027
LogS:  -2.732
# Rotatable Bonds:  9
TPSA:  52.6
# H-Bond Aceptor:  4
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.373
Synthetic Accessibility Score:  2.02
Fsp3:  0.8
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.41
MDCK Permeability:  4.009386248071678e-05
Pgp-inhibitor:  0.08
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.002
20% Bioavailability (F20%):  0.995
30% Bioavailability (F30%):  0.992

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.305
Plasma Protein Binding (PPB):  85.18528747558594%
Volume Distribution (VD):  0.46
Pgp-substrate:  16.91484832763672%

ADMET: Metabolism

CYP1A2-inhibitor:  0.976
CYP1A2-substrate:  0.599
CYP2C19-inhibitor:  0.807
CYP2C19-substrate:  0.272
CYP2C9-inhibitor:  0.528
CYP2C9-substrate:  0.208
CYP2D6-inhibitor:  0.092
CYP2D6-substrate:  0.117
CYP3A4-inhibitor:  0.094
CYP3A4-substrate:  0.161

ADMET: Excretion

Clearance (CL):  12.279
Half-life (T1/2):  0.611

ADMET: Toxicity

hERG Blockers:  0.173
Human Hepatotoxicity (H-HT):  0.008
Drug-inuced Liver Injury (DILI):  0.044
AMES Toxicity:  0.01
Rat Oral Acute Toxicity:  0.004
Maximum Recommended Daily Dose:  0.007
Skin Sensitization:  0.878
Carcinogencity:  0.052
Eye Corrosion:  0.947
Eye Irritation:  0.99
Respiratory Toxicity:  0.069

Download Data

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

  Natural Product: NPC140229

Natural Product ID:  NPC140229
Common Name*:   Dibutyl Oxalate
IUPAC Name:   dibutyl oxalate
Synonyms:  
Standard InCHIKey:  JKRZOJADNVOXPM-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C10H18O4/c1-3-5-7-13-9(11)10(12)14-8-6-4-2/h3-8H2,1-2H3
SMILES:  CCCCOC(=O)C(=O)OCCCC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3185643
PubChem CID:   16306
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0000346] Dicarboxylic acids and derivatives

*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
NPO210 Uvaria calamistrata Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[10075755]
NPO210 Uvaria calamistrata Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[11000019]
NPO11248 Tachigalia paniculata n.a. n.a. n.a. leaves n.a. n.a. PMID[12444671]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. leaf n.a. PMID[18409045]
NPO29141 Panax ginseng Species Araliaceae Eukaryota flower buds n.a. n.a. PMID[19926279]
NPO10540 Passiflora incarnata Species Passifloraceae Eukaryota n.a. n.a. n.a. PMID[2026709]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. root n.a. PMID[2092947]
NPO29141 Panax ginseng Species Araliaceae Eukaryota berry n.a. n.a. PMID[21216145]
NPO29141 Panax ginseng Species Araliaceae Eukaryota leaves n.a. n.a. PMID[24290061]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[24968750]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[25152999]
NPO29141 Panax ginseng Species Araliaceae Eukaryota stems-leaves n.a. n.a. PMID[26420067]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. stem n.a. PMID[27914541]
NPO29141 Panax ginseng Species Araliaceae Eukaryota Flower Buds n.a. n.a. PMID[28345906]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[32129622]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10540 Passiflora incarnata Species Passifloraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO10540 Passiflora incarnata Species Passifloraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO13166 Nicotiana undulata Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO731 Panax schinseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11248 Tachigalia paniculata n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO11488 Alstonia muelleriana Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14354 Artemisia cina Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5189 Glycine tomentella Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12001 Saccharomyces pastori Species Saccharomycetaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10540 Passiflora incarnata Species Passifloraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21854 Pterocladiella tenuis Species Gelidiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18805 Tripolium pannonicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11642 Dacrydium cupressinum Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO210 Uvaria calamistrata Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14255 Streptomyces flocculus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO12684 Trigonella grandiflora Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19635 Coreopsis nodosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13568 Hypoxylon rubiginosum Species Xylariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7998 Senecio paludaffinis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22666 Haematococcus lacustris Species Haematococcaceae 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
NPT2 Others Unspecified Potency n.a. 611.3 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 21872.4 nM PubChem BioAssay data set

☑ 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 NPC140229 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
0.871 High Similarity NPC232172
0.7647 Intermediate Similarity NPC281883
0.7632 Intermediate Similarity NPC474205
0.7632 Intermediate Similarity NPC225963
0.7419 Intermediate Similarity NPC3693
0.7353 Intermediate Similarity NPC5934
0.7273 Intermediate Similarity NPC88135
0.7188 Intermediate Similarity NPC166804
0.7143 Intermediate Similarity NPC12904
0.7143 Intermediate Similarity NPC40965
0.7097 Intermediate Similarity NPC110107
0.7073 Intermediate Similarity NPC144829
0.7059 Intermediate Similarity NPC127696
0.697 Remote Similarity NPC143211
0.697 Remote Similarity NPC248233
0.6944 Remote Similarity NPC108238
0.6944 Remote Similarity NPC41007
0.6944 Remote Similarity NPC178643
0.6944 Remote Similarity NPC168714
0.6944 Remote Similarity NPC35371
0.6944 Remote Similarity NPC286695
0.6944 Remote Similarity NPC322892
0.6875 Remote Similarity NPC32280
0.6875 Remote Similarity NPC41485
0.6842 Remote Similarity NPC24967
0.6842 Remote Similarity NPC103612
0.6774 Remote Similarity NPC23508
0.6765 Remote Similarity NPC316272
0.6765 Remote Similarity NPC281943
0.6765 Remote Similarity NPC317739
0.6757 Remote Similarity NPC154396
0.6757 Remote Similarity NPC286498
0.6667 Remote Similarity NPC201132
0.6667 Remote Similarity NPC127134
0.6596 Remote Similarity NPC287811
0.6579 Remote Similarity NPC223374
0.6579 Remote Similarity NPC196442
0.6579 Remote Similarity NPC301398
0.6579 Remote Similarity NPC325165
0.6579 Remote Similarity NPC155872
0.6579 Remote Similarity NPC86545
0.641 Remote Similarity NPC80396
0.641 Remote Similarity NPC80641
0.641 Remote Similarity NPC154642
0.6389 Remote Similarity NPC21374
0.6389 Remote Similarity NPC265882
0.6364 Remote Similarity NPC28246
0.6341 Remote Similarity NPC81263
0.6286 Remote Similarity NPC238135
0.625 Remote Similarity NPC14608
0.625 Remote Similarity NPC8187
0.625 Remote Similarity NPC128996
0.625 Remote Similarity NPC203105
0.6176 Remote Similarity NPC211250
0.617 Remote Similarity NPC477778
0.6129 Remote Similarity NPC61373
0.6111 Remote Similarity NPC180423
0.6111 Remote Similarity NPC312003
0.6098 Remote Similarity NPC316546
0.6087 Remote Similarity NPC474204
0.6061 Remote Similarity NPC8368
0.6047 Remote Similarity NPC53541
0.6047 Remote Similarity NPC159773
0.6042 Remote Similarity NPC301482
0.6 Remote Similarity NPC5505
0.5952 Remote Similarity NPC80234
0.5909 Remote Similarity NPC325102
0.5897 Remote Similarity NPC57499
0.5833 Remote Similarity NPC55956
0.5833 Remote Similarity NPC234005
0.5833 Remote Similarity NPC473551
0.5814 Remote Similarity NPC149299
0.5814 Remote Similarity NPC40597
0.5814 Remote Similarity NPC250028
0.5814 Remote Similarity NPC256163
0.5806 Remote Similarity NPC43196
0.5806 Remote Similarity NPC37493
0.5758 Remote Similarity NPC208021
0.5714 Remote Similarity NPC230452
0.5714 Remote Similarity NPC55678
0.5714 Remote Similarity NPC317724
0.5714 Remote Similarity NPC329496
0.5714 Remote Similarity NPC128335
0.5686 Remote Similarity NPC477780
0.5686 Remote Similarity NPC477781
0.5641 Remote Similarity NPC99700
0.5641 Remote Similarity NPC147054
0.5641 Remote Similarity NPC217218
0.561 Remote Similarity NPC65353
0.561 Remote Similarity NPC233231
0.561 Remote Similarity NPC321699

  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 NPC140229 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
0.7647 Intermediate Similarity NPD9636 Phase 2
0.7353 Intermediate Similarity NPD8856 Phase 2
0.7222 Intermediate Similarity NPD900 Approved
0.6667 Remote Similarity NPD8989 Approved
0.625 Remote Similarity NPD9131 Discovery
0.5957 Remote Similarity NPD6125 Clinical (unspecified phase)
0.5806 Remote Similarity NPD7357 Approved
0.5806 Remote Similarity NPD7356 Approved
0.5652 Remote Similarity NPD377 Approved
0.56 Remote Similarity NPD1400 Approved
0.56 Remote Similarity NPD1399 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