Structure

Physi-Chem Properties

Molecular Weight:  172.07
Volume:  174.176
LogP:  1.399
LogD:  1.062
LogS:  -2.163
# Rotatable Bonds:  6
TPSA:  52.6
# H-Bond Aceptor:  4
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.462
Synthetic Accessibility Score:  2.016
Fsp3:  0.5
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.284
MDCK Permeability:  7.384213677141815e-05
Pgp-inhibitor:  0.002
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.327
30% Bioavailability (F30%):  0.99

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.621
Plasma Protein Binding (PPB):  55.166927337646484%
Volume Distribution (VD):  0.757
Pgp-substrate:  41.615604400634766%

ADMET: Metabolism

CYP1A2-inhibitor:  0.982
CYP1A2-substrate:  0.174
CYP2C19-inhibitor:  0.582
CYP2C19-substrate:  0.38
CYP2C9-inhibitor:  0.434
CYP2C9-substrate:  0.93
CYP2D6-inhibitor:  0.214
CYP2D6-substrate:  0.241
CYP3A4-inhibitor:  0.145
CYP3A4-substrate:  0.235

ADMET: Excretion

Clearance (CL):  9.275
Half-life (T1/2):  0.793

ADMET: Toxicity

hERG Blockers:  0.004
Human Hepatotoxicity (H-HT):  0.015
Drug-inuced Liver Injury (DILI):  0.19
AMES Toxicity:  0.035
Rat Oral Acute Toxicity:  0.02
Maximum Recommended Daily Dose:  0.008
Skin Sensitization:  0.946
Carcinogencity:  0.193
Eye Corrosion:  0.982
Eye Irritation:  0.977
Respiratory Toxicity:  0.043

Download Data

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

  Natural Product: NPC281043

Natural Product ID:  NPC281043
Common Name*:   Diethyl (E)-But-2-Enedioate
IUPAC Name:   diethyl (E)-but-2-enedioate
Synonyms:  
Standard InCHIKey:  IEPRKVQEAMIZSS-AATRIKPKSA-N
Standard InCHI:  InChI=1S/C8H12O4/c1-3-11-7(9)5-6-8(10)12-4-2/h5-6H,3-4H2,1-2H3/b6-5+
SMILES:  CCOC(=O)/C=C/C(=O)OCC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3187857
PubChem CID:   638144
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000324] Fatty acid esters

*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
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. Nigeria(latitude 80°N and longitude 4°E) 2005; 2006 DOI[10.1002/ejlt.201000080]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s11306-010-0259-y]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s11306-014-0638-x]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s11746-997-0093-1]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.phytol.2008.07.007]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Seeds Plovdiv, Plovdiv region in South Bulgaria DOI[10.1051/CTV/20163101031]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. PMID[11170689]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. fruit n.a. PMID[11312782]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. leaf n.a. PMID[11312782]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. PMID[11408943]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. fruit n.a. PMID[12105962]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. Esuela Tecnica Superior de Ingenieros Agrónomos de Albacete 2007 PMID[19256538]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. PMID[20826702]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. PMID[22537213]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. PMID[23759170]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Stalks n.a. n.a. PMID[24521157]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Seeds Benedictine Pannonhalma Archabbey, Hungary PMID[29803478]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. PMID[31433178]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Leaf Essent. Oil n.a. n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Fruits n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17024 Vitis vinifera Species Vitaceae 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
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens Potency n.a. 12197.2 nM PubChem BioAssay data set
NPT20 Organism Candida albicans Candida albicans MIC = 60.0 ug.mL-1 PMID[568435]
NPT20 Organism Candida albicans Candida albicans MIC = 70.0 ug.mL-1 PMID[568435]
NPT20 Organism Candida albicans Candida albicans MIC = 90.0 ug.mL-1 PMID[568435]
NPT769 Organism Mucor mucedo Mucor mucedo MIC = 40.0 ug.mL-1 PMID[568435]
NPT769 Organism Mucor mucedo Mucor mucedo MIC = 50.0 ug.mL-1 PMID[568435]
NPT330 Organism Trichophyton mentagrophytes Trichophyton mentagrophytes MIC = 7.0 ug.mL-1 PMID[568435]
NPT330 Organism Trichophyton mentagrophytes Trichophyton mentagrophytes MIC = 20.0 ug.mL-1 PMID[568435]
NPT330 Organism Trichophyton mentagrophytes Trichophyton mentagrophytes MIC = 18.0 ug.mL-1 PMID[568435]
NPT330 Organism Trichophyton mentagrophytes Trichophyton mentagrophytes MIC = 50.0 ug.mL-1 PMID[568435]
NPT2 Others Unspecified Ki = 11100.0 nM PMID[568436]
NPT2 Others Unspecified Activity = 34.3 % PMID[568436]
NPT2 Others Unspecified Ki = 21700.0 nM PMID[568436]
NPT2 Others Unspecified Ki = 12000.0 nM PMID[568436]
NPT2 Others Unspecified Potency n.a. 21880.4 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 24336.5 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 48557.7 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 24550.3 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 17380.2 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 NPC281043 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
0.9 High Similarity NPC41409
0.85 High Similarity NPC297608
0.85 High Similarity NPC250954
0.8421 Intermediate Similarity NPC65353
0.825 Intermediate Similarity NPC298413
0.825 Intermediate Similarity NPC147824
0.7895 Intermediate Similarity NPC63354
0.7692 Intermediate Similarity NPC122676
0.7674 Intermediate Similarity NPC57923
0.766 Intermediate Similarity NPC15789
0.7442 Intermediate Similarity NPC159773
0.7297 Intermediate Similarity NPC323552
0.7292 Intermediate Similarity NPC236338
0.7292 Intermediate Similarity NPC275316
0.7234 Intermediate Similarity NPC90490
0.7209 Intermediate Similarity NPC203382
0.7083 Intermediate Similarity NPC82446
0.7 Intermediate Similarity NPC98098
0.7 Intermediate Similarity NPC224651
0.6981 Remote Similarity NPC294938
0.6981 Remote Similarity NPC129150
0.6875 Remote Similarity NPC128520
0.6852 Remote Similarity NPC254095
0.6852 Remote Similarity NPC223679
0.6829 Remote Similarity NPC60675
0.6829 Remote Similarity NPC297363
0.6809 Remote Similarity NPC270706
0.6809 Remote Similarity NPC47946
0.6809 Remote Similarity NPC26600
0.6792 Remote Similarity NPC150717
0.6744 Remote Similarity NPC226511
0.6744 Remote Similarity NPC63598
0.6731 Remote Similarity NPC151761
0.6731 Remote Similarity NPC159535
0.6727 Remote Similarity NPC82465
0.6727 Remote Similarity NPC97570
0.6667 Remote Similarity NPC197467
0.6667 Remote Similarity NPC128280
0.6667 Remote Similarity NPC135863
0.6667 Remote Similarity NPC249850
0.6667 Remote Similarity NPC9290
0.6667 Remote Similarity NPC293437
0.6607 Remote Similarity NPC26223
0.6596 Remote Similarity NPC312547
0.6545 Remote Similarity NPC21946
0.6522 Remote Similarity NPC102879
0.6512 Remote Similarity NPC107877
0.6491 Remote Similarity NPC26810
0.6481 Remote Similarity NPC230296
0.6481 Remote Similarity NPC221763
0.6481 Remote Similarity NPC245002
0.6458 Remote Similarity NPC172042
0.6444 Remote Similarity NPC8270
0.6444 Remote Similarity NPC123357
0.6429 Remote Similarity NPC159650
0.6429 Remote Similarity NPC302564
0.6429 Remote Similarity NPC22897
0.6415 Remote Similarity NPC478120
0.64 Remote Similarity NPC135698
0.6379 Remote Similarity NPC474774
0.6346 Remote Similarity NPC106531
0.6346 Remote Similarity NPC191643
0.6316 Remote Similarity NPC309408
0.6316 Remote Similarity NPC79756
0.6316 Remote Similarity NPC98519
0.6316 Remote Similarity NPC130953
0.6304 Remote Similarity NPC221250
0.6296 Remote Similarity NPC474913
0.6279 Remote Similarity NPC308418
0.6271 Remote Similarity NPC308457
0.6271 Remote Similarity NPC25747
0.6271 Remote Similarity NPC470808
0.6271 Remote Similarity NPC148233
0.625 Remote Similarity NPC51329
0.625 Remote Similarity NPC189700
0.6226 Remote Similarity NPC477780
0.6226 Remote Similarity NPC477781
0.62 Remote Similarity NPC68577
0.619 Remote Similarity NPC146507
0.619 Remote Similarity NPC310810
0.6182 Remote Similarity NPC86948
0.617 Remote Similarity NPC187922
0.6167 Remote Similarity NPC273600
0.6167 Remote Similarity NPC96414
0.6167 Remote Similarity NPC19769
0.6111 Remote Similarity NPC269615
0.6102 Remote Similarity NPC179087
0.6102 Remote Similarity NPC68110
0.6102 Remote Similarity NPC473737
0.6102 Remote Similarity NPC210303
0.6102 Remote Similarity NPC44343
0.6078 Remote Similarity NPC234084
0.6078 Remote Similarity NPC223675
0.6078 Remote Similarity NPC126184
0.6078 Remote Similarity NPC250919
0.6071 Remote Similarity NPC471279
0.6071 Remote Similarity NPC471277
0.6066 Remote Similarity NPC276299
0.6066 Remote Similarity NPC146811
0.6066 Remote Similarity NPC201356
0.6066 Remote Similarity NPC475675
0.6066 Remote Similarity NPC475555
0.6066 Remote Similarity NPC124586
0.6 Remote Similarity NPC173157
0.6 Remote Similarity NPC478117
0.6 Remote Similarity NPC8466
0.5968 Remote Similarity NPC122627
0.5965 Remote Similarity NPC474084
0.5952 Remote Similarity NPC144407
0.5946 Remote Similarity NPC110107
0.5932 Remote Similarity NPC151648
0.5932 Remote Similarity NPC263732
0.5932 Remote Similarity NPC15193
0.5918 Remote Similarity NPC12907
0.5893 Remote Similarity NPC51846
0.5873 Remote Similarity NPC63873
0.5873 Remote Similarity NPC475760
0.5862 Remote Similarity NPC286189
0.5862 Remote Similarity NPC474267
0.5849 Remote Similarity NPC43053
0.5833 Remote Similarity NPC2328
0.5818 Remote Similarity NPC218486
0.5806 Remote Similarity NPC248125
0.5789 Remote Similarity NPC32280
0.5789 Remote Similarity NPC3693
0.5789 Remote Similarity NPC265551
0.5789 Remote Similarity NPC41485
0.5789 Remote Similarity NPC212730
0.5781 Remote Similarity NPC475982
0.5781 Remote Similarity NPC151481
0.5769 Remote Similarity NPC15912
0.5763 Remote Similarity NPC299730
0.575 Remote Similarity NPC20903
0.5741 Remote Similarity NPC310746
0.5714 Remote Similarity NPC203335
0.5714 Remote Similarity NPC225272
0.5714 Remote Similarity NPC40805
0.5714 Remote Similarity NPC273054
0.5714 Remote Similarity NPC281883
0.5714 Remote Similarity NPC103560
0.5692 Remote Similarity NPC476037
0.5692 Remote Similarity NPC476012
0.569 Remote Similarity NPC478096
0.5682 Remote Similarity NPC72258
0.5676 Remote Similarity NPC23508
0.5667 Remote Similarity NPC55376
0.566 Remote Similarity NPC27264
0.566 Remote Similarity NPC221467
0.5645 Remote Similarity NPC470123
0.5645 Remote Similarity NPC133904
0.5645 Remote Similarity NPC282760
0.5645 Remote Similarity NPC476589
0.5645 Remote Similarity NPC182794
0.5641 Remote Similarity NPC127134
0.5641 Remote Similarity NPC166804
0.5641 Remote Similarity NPC201132
0.5636 Remote Similarity NPC327103
0.5625 Remote Similarity NPC477117
0.5625 Remote Similarity NPC218477
0.5614 Remote Similarity NPC96663
0.5614 Remote Similarity NPC472808
0.5614 Remote Similarity NPC324224
0.561 Remote Similarity NPC127696
0.5606 Remote Similarity NPC293114
0.5606 Remote Similarity NPC475762
0.5606 Remote Similarity NPC316185
0.56 Remote Similarity NPC6963
0.56 Remote Similarity NPC304079

  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 NPC281043 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
0.9189 High Similarity NPD9115 Approved
0.7 Intermediate Similarity NPD8573 Approved
0.6458 Remote Similarity NPD9378 Approved
0.625 Remote Similarity NPD9114 Clinical (unspecified phase)
0.6154 Remote Similarity NPD6927 Phase 3
0.5962 Remote Similarity NPD9437 Clinical (unspecified phase)
0.5918 Remote Similarity NPD6097 Approved
0.5918 Remote Similarity NPD6096 Approved
0.575 Remote Similarity NPD8187 Phase 3
0.5745 Remote Similarity NPD8839 Phase 3
0.5714 Remote Similarity NPD9636 Phase 2
0.5641 Remote Similarity NPD8989 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