Structure

Physi-Chem Properties

Molecular Weight:  84.06
Volume:  98.554
LogP:  0.68
LogD:  0.735
LogS:  -0.419
# Rotatable Bonds:  2
TPSA:  17.07
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.362
Synthetic Accessibility Score:  3.107
Fsp3:  0.4
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.166
MDCK Permeability:  4.040870044264011e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.004
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.005
30% Bioavailability (F30%):  0.09

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.998
Plasma Protein Binding (PPB):  43.83811950683594%
Volume Distribution (VD):  0.942
Pgp-substrate:  69.34880065917969%

ADMET: Metabolism

CYP1A2-inhibitor:  0.401
CYP1A2-substrate:  0.767
CYP2C19-inhibitor:  0.076
CYP2C19-substrate:  0.798
CYP2C9-inhibitor:  0.015
CYP2C9-substrate:  0.921
CYP2D6-inhibitor:  0.013
CYP2D6-substrate:  0.874
CYP3A4-inhibitor:  0.009
CYP3A4-substrate:  0.166

ADMET: Excretion

Clearance (CL):  6.51
Half-life (T1/2):  0.739

ADMET: Toxicity

hERG Blockers:  0.013
Human Hepatotoxicity (H-HT):  0.104
Drug-inuced Liver Injury (DILI):  0.055
AMES Toxicity:  0.891
Rat Oral Acute Toxicity:  0.659
Maximum Recommended Daily Dose:  0.052
Skin Sensitization:  0.932
Carcinogencity:  0.889
Eye Corrosion:  0.98
Eye Irritation:  0.995
Respiratory Toxicity:  0.887

Download Data

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

  Natural Product: NPC72258

Natural Product ID:  NPC72258
Common Name*:   Pentenal
IUPAC Name:   (E)-pent-2-enal
Synonyms:   2-Pentenal; Pent-2-enal
Standard InCHIKey:  DTCCTIQRPGSLPT-ONEGZZNKSA-N
Standard InCHI:  InChI=1S/C5H8O/c1-2-3-4-5-6/h3-5H,2H2,1H3/b4-3+
SMILES:  CC/C=C/C=O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL256368
PubChem CID:   5364752
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0003131] Alpha,beta-unsaturated carbonyl compounds
            • [CHEMONTID:0002433] Alpha,beta-unsaturated aldehydes
              • [CHEMONTID:0002436] Enals

*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
NPO26429 Capsella bursa-pastoris Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23332.1 Dendrobium fimbriatum var. oculatum Varieties Orchidaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11889 Dendrobium chrysanthum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23768 Camellia saluenensis Species Theaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26429 Capsella bursa-pastoris Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23332.1 Dendrobium fimbriatum var. oculatum Varieties Orchidaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26429 Capsella bursa-pastoris Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO11889 Dendrobium chrysanthum Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO26429 Capsella bursa-pastoris Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23768 Camellia saluenensis Species Theaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11889 Dendrobium chrysanthum Species Orchidaceae 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
NPT346 Individual Protein Transient receptor potential cation channel subfamily A member 1 Homo sapiens EC50 = 5000.0 nM PMID[476785]
NPT346 Individual Protein Transient receptor potential cation channel subfamily A member 1 Homo sapiens EC50 = 5000.0 nM PMID[476786]
NPT348 Organism Myzus persicae Myzus persicae LD90 = 25.8 mg/L PMID[476787]
NPT348 Organism Myzus persicae Myzus persicae CTP = 106.0 mg/L.hr PMID[476787]
NPT348 Organism Myzus persicae Myzus persicae LD50 = 13.1 mg/L PMID[476787]
NPT563 Organism Escherichia coli O157:H7 Escherichia coli O157:H7 GI = 11.0 % PMID[476788]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus GI = 12.2 % PMID[476788]
NPT564 Organism Listeria monocytogenes Listeria monocytogenes GI = 16.9 % PMID[476788]
NPT565 Organism Vibrio parahaemolyticus Vibrio parahaemolyticus GI = 40.7 % PMID[476788]
NPT566 Organism Salmonella typhimurium Salmonella enterica subsp. enterica serovar Typhimurium GI = 39.6 % PMID[476788]
NPT314 Organism Bacillus cereus Bacillus cereus GI = 27.4 % PMID[476788]
NPT35 Others n.a. K = 28.3 /M/s PMID[476789]

☑ 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 NPC72258 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
0.9697 High Similarity NPC75204
0.9412 High Similarity NPC8416
0.9412 High Similarity NPC279300
0.8889 High Similarity NPC33761
0.8857 High Similarity NPC254764
0.8649 High Similarity NPC323278
0.8438 Intermediate Similarity NPC8466
0.8421 Intermediate Similarity NPC33489
0.8235 Intermediate Similarity NPC144407
0.8205 Intermediate Similarity NPC208936
0.8205 Intermediate Similarity NPC287397
0.8205 Intermediate Similarity NPC67920
0.8205 Intermediate Similarity NPC298710
0.8158 Intermediate Similarity NPC101147
0.8158 Intermediate Similarity NPC18205
0.8158 Intermediate Similarity NPC12319
0.8 Intermediate Similarity NPC146507
0.7941 Intermediate Similarity NPC273054
0.7714 Intermediate Similarity NPC109034
0.75 Intermediate Similarity NPC310810
0.7297 Intermediate Similarity NPC269641
0.7273 Intermediate Similarity NPC324812
0.7222 Intermediate Similarity NPC266979
0.7188 Intermediate Similarity NPC235797
0.7027 Intermediate Similarity NPC12889
0.7 Intermediate Similarity NPC217923
0.6829 Remote Similarity NPC8270
0.6757 Remote Similarity NPC63121
0.6757 Remote Similarity NPC197356
0.6757 Remote Similarity NPC304788
0.675 Remote Similarity NPC226511
0.6739 Remote Similarity NPC477789
0.6667 Remote Similarity NPC221250
0.6579 Remote Similarity NPC250734
0.65 Remote Similarity NPC24833
0.6471 Remote Similarity NPC94980
0.6458 Remote Similarity NPC30433
0.6458 Remote Similarity NPC234829
0.6444 Remote Similarity NPC239754
0.6429 Remote Similarity NPC123357
0.6429 Remote Similarity NPC111474
0.6429 Remote Similarity NPC113082
0.641 Remote Similarity NPC58957
0.6389 Remote Similarity NPC155900
0.6364 Remote Similarity NPC106819
0.6364 Remote Similarity NPC216921
0.6304 Remote Similarity NPC110234
0.6304 Remote Similarity NPC44363
0.6304 Remote Similarity NPC163751
0.6279 Remote Similarity NPC270170
0.6279 Remote Similarity NPC7754
0.6275 Remote Similarity NPC317899
0.625 Remote Similarity NPC275316
0.625 Remote Similarity NPC15789
0.6222 Remote Similarity NPC267514
0.6222 Remote Similarity NPC114841
0.6222 Remote Similarity NPC145755
0.6154 Remote Similarity NPC477790
0.6136 Remote Similarity NPC187922
0.6136 Remote Similarity NPC57923
0.6087 Remote Similarity NPC158853
0.6078 Remote Similarity NPC209431
0.6078 Remote Similarity NPC100809
0.6038 Remote Similarity NPC281986
0.6038 Remote Similarity NPC321568
0.6038 Remote Similarity NPC208749
0.6038 Remote Similarity NPC22019
0.5962 Remote Similarity NPC188789
0.5957 Remote Similarity NPC276009
0.5957 Remote Similarity NPC22098
0.5957 Remote Similarity NPC195246
0.5952 Remote Similarity NPC40434
0.5952 Remote Similarity NPC92863
0.5952 Remote Similarity NPC34873
0.5952 Remote Similarity NPC155880
0.5952 Remote Similarity NPC130923
0.5918 Remote Similarity NPC236338
0.587 Remote Similarity NPC477686
0.587 Remote Similarity NPC106547
0.587 Remote Similarity NPC471753
0.5854 Remote Similarity NPC38497
0.5818 Remote Similarity NPC82465
0.5814 Remote Similarity NPC277382
0.5814 Remote Similarity NPC15934
0.5814 Remote Similarity NPC171978
0.5769 Remote Similarity NPC300121
0.5745 Remote Similarity NPC191337
0.5745 Remote Similarity NPC474362
0.5745 Remote Similarity NPC474202
0.5745 Remote Similarity NPC110396
0.5745 Remote Similarity NPC270706
0.5745 Remote Similarity NPC166788
0.5714 Remote Similarity NPC185839
0.5714 Remote Similarity NPC195109
0.5682 Remote Similarity NPC48930
0.5682 Remote Similarity NPC297608
0.5682 Remote Similarity NPC281043
0.5652 Remote Similarity NPC292463
0.5652 Remote Similarity NPC301972
0.5636 Remote Similarity NPC21946
0.5625 Remote Similarity NPC128280
0.5625 Remote Similarity NPC471752
0.5625 Remote Similarity NPC100380
0.561 Remote Similarity NPC60675
0.561 Remote Similarity NPC297363
0.56 Remote Similarity NPC118788
0.56 Remote Similarity NPC221467
0.56 Remote Similarity NPC288381
0.56 Remote Similarity NPC220191
0.56 Remote Similarity NPC225974
0.56 Remote Similarity NPC15325
0.56 Remote Similarity NPC20934

  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 NPC72258 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
0.6512 Remote Similarity NPD9297 Discontinued
0.6512 Remote Similarity NPD9091 Suspended
0.6087 Remote Similarity NPD9090 Phase 3
0.587 Remote Similarity NPD6096 Approved
0.587 Remote Similarity NPD6097 Approved
0.5714 Remote Similarity NPD9115 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