Structure

Physi-Chem Properties

Molecular Weight:  128.12
Volume:  153.078
LogP:  2.755
LogD:  2.534
LogS:  -2.123
# Rotatable Bonds:  5
TPSA:  17.07
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.519
Synthetic Accessibility Score:  3.028
Fsp3:  0.875
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:  -4.327
MDCK Permeability:  2.3948177840793505e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.466
30% Bioavailability (F30%):  0.67

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.991
Plasma Protein Binding (PPB):  43.31451416015625%
Volume Distribution (VD):  2.421
Pgp-substrate:  57.15441131591797%

ADMET: Metabolism

CYP1A2-inhibitor:  0.471
CYP1A2-substrate:  0.866
CYP2C19-inhibitor:  0.065
CYP2C19-substrate:  0.687
CYP2C9-inhibitor:  0.036
CYP2C9-substrate:  0.37
CYP2D6-inhibitor:  0.211
CYP2D6-substrate:  0.417
CYP3A4-inhibitor:  0.166
CYP3A4-substrate:  0.235

ADMET: Excretion

Clearance (CL):  8.554
Half-life (T1/2):  0.754

ADMET: Toxicity

hERG Blockers:  0.075
Human Hepatotoxicity (H-HT):  0.02
Drug-inuced Liver Injury (DILI):  0.049
AMES Toxicity:  0.01
Rat Oral Acute Toxicity:  0.016
Maximum Recommended Daily Dose:  0.041
Skin Sensitization:  0.958
Carcinogencity:  0.171
Eye Corrosion:  0.994
Eye Irritation:  0.991
Respiratory Toxicity:  0.825

Download Data

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

  Natural Product: NPC218357

Natural Product ID:  NPC218357
Common Name*:   2-Ethylhexanal
IUPAC Name:   2-ethylhexanal
Synonyms:  
Standard InCHIKey:  LGYNIFWIKSEESD-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C8H16O/c1-3-5-6-8(4-2)7-9/h7-8H,3-6H2,1-2H3
SMILES:  CCCCC(C=O)CC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1558074
PubChem CID:   31241
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0000124] Aldehydes
            • [CHEMONTID:0002229] Medium-chain aldehydes

*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
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota Leaves n.a. n.a. PMID[12088434]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[21707257]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota Essential Oil n.a. n.a. Database[FooDB]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO11411 Gossypium herbaceum Species Malvaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12935 Thymus quinquecostatus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO11411 Gossypium herbaceum Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12935 Thymus quinquecostatus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO12935 Thymus quinquecostatus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO19472 Thymus vulgaris Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12935 Thymus quinquecostatus Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11411 Gossypium herbaceum Species Malvaceae 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
NPT347 Cell Line Lymphoblastoid cells Homo sapiens Potency = 1000.0 nM PMID[564990]
NPT210 Individual Protein Thyroid stimulating hormone receptor Homo sapiens Potency = 31.6 nM PMID[564990]
NPT93 Individual Protein Survival motor neuron protein Homo sapiens Potency = 12589.3 nM PMID[564990]
NPT2 Others Unspecified Potency n.a. 77742.1 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 5792.5 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 55519.6 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 19527.9 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 NPC218357 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
0.8857 High Similarity NPC69245
0.8125 Intermediate Similarity NPC287782
0.7941 Intermediate Similarity NPC262505
0.7941 Intermediate Similarity NPC49151
0.7941 Intermediate Similarity NPC254713
0.7941 Intermediate Similarity NPC179831
0.7941 Intermediate Similarity NPC261991
0.7576 Intermediate Similarity NPC32279
0.75 Intermediate Similarity NPC49615
0.75 Intermediate Similarity NPC59581
0.7273 Intermediate Similarity NPC13105
0.7188 Intermediate Similarity NPC289974
0.7188 Intermediate Similarity NPC304927
0.7179 Intermediate Similarity NPC223315
0.7143 Intermediate Similarity NPC321646
0.7105 Intermediate Similarity NPC301919
0.7045 Intermediate Similarity NPC276009
0.7045 Intermediate Similarity NPC195246
0.7045 Intermediate Similarity NPC22098
0.6875 Remote Similarity NPC164646
0.6829 Remote Similarity NPC135077
0.6829 Remote Similarity NPC59570
0.6829 Remote Similarity NPC215118
0.6829 Remote Similarity NPC45270
0.6818 Remote Similarity NPC308301
0.6765 Remote Similarity NPC100997
0.6667 Remote Similarity NPC248763
0.6667 Remote Similarity NPC325452
0.6585 Remote Similarity NPC141634
0.6585 Remote Similarity NPC3531
0.6579 Remote Similarity NPC248190
0.6571 Remote Similarity NPC295442
0.6562 Remote Similarity NPC133819
0.6512 Remote Similarity NPC18397
0.6444 Remote Similarity NPC282440
0.641 Remote Similarity NPC121215
0.6389 Remote Similarity NPC222997
0.6389 Remote Similarity NPC4962
0.6389 Remote Similarity NPC42403
0.6389 Remote Similarity NPC196434
0.6389 Remote Similarity NPC29561
0.6389 Remote Similarity NPC221192
0.6389 Remote Similarity NPC153439
0.6389 Remote Similarity NPC79887
0.6364 Remote Similarity NPC106819
0.6341 Remote Similarity NPC316546
0.6327 Remote Similarity NPC22182
0.6304 Remote Similarity NPC249754
0.625 Remote Similarity NPC37479
0.625 Remote Similarity NPC305182
0.6216 Remote Similarity NPC168982
0.619 Remote Similarity NPC81263
0.6176 Remote Similarity NPC307594
0.6176 Remote Similarity NPC66624
0.6176 Remote Similarity NPC227197
0.6154 Remote Similarity NPC283682
0.6111 Remote Similarity NPC38859
0.6111 Remote Similarity NPC198118
0.6098 Remote Similarity NPC14608
0.6087 Remote Similarity NPC314679
0.6078 Remote Similarity NPC95581
0.6078 Remote Similarity NPC250539
0.6078 Remote Similarity NPC209431
0.6078 Remote Similarity NPC100809
0.6053 Remote Similarity NPC16578
0.6053 Remote Similarity NPC149101
0.6053 Remote Similarity NPC268596
0.6053 Remote Similarity NPC225318
0.6053 Remote Similarity NPC76608
0.6047 Remote Similarity NPC48930
0.6 Remote Similarity NPC171783
0.6 Remote Similarity NPC79591
0.5962 Remote Similarity NPC188789
0.5957 Remote Similarity NPC40249
0.5957 Remote Similarity NPC14917
0.5957 Remote Similarity NPC4079
0.5957 Remote Similarity NPC131981
0.5957 Remote Similarity NPC83187
0.5957 Remote Similarity NPC98246
0.5957 Remote Similarity NPC285814
0.5957 Remote Similarity NPC236355
0.5957 Remote Similarity NPC173996
0.5897 Remote Similarity NPC178643
0.5897 Remote Similarity NPC35371
0.5897 Remote Similarity NPC41007
0.5897 Remote Similarity NPC168714
0.5882 Remote Similarity NPC91093
0.587 Remote Similarity NPC114841
0.587 Remote Similarity NPC55023
0.5854 Remote Similarity NPC154642
0.5854 Remote Similarity NPC80396
0.5833 Remote Similarity NPC294440
0.5833 Remote Similarity NPC324793
0.5833 Remote Similarity NPC477878
0.5814 Remote Similarity NPC80234
0.58 Remote Similarity NPC314084
0.5745 Remote Similarity NPC239754
0.5714 Remote Similarity NPC258672
0.5714 Remote Similarity NPC293343
0.5714 Remote Similarity NPC177022
0.5714 Remote Similarity NPC252843
0.5714 Remote Similarity NPC247786
0.5682 Remote Similarity NPC256163
0.5682 Remote Similarity NPC250028
0.5682 Remote Similarity NPC40597
0.5682 Remote Similarity NPC149299
0.5625 Remote Similarity NPC163751
0.5625 Remote Similarity NPC110234
0.5625 Remote Similarity NPC21844
0.5625 Remote Similarity NPC44363
0.561 Remote Similarity NPC155872
0.56 Remote Similarity NPC32351

  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 NPC218357 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
0.6923 Remote Similarity NPD9449 Clinical (unspecified phase)
0.6842 Remote Similarity NPD9447 Approved
0.6585 Remote Similarity NPD77 Approved
0.6585 Remote Similarity NPD9450 Approved
0.6087 Remote Similarity NPD634 Phase 3
0.5957 Remote Similarity NPD343 Approved
0.5957 Remote Similarity NPD345 Approved
0.5957 Remote Similarity NPD344 Approved
0.5778 Remote Similarity NPD387 Clinical (unspecified phase)
0.5682 Remote Similarity NPD9635 Discontinued

  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