Structure

Physi-Chem Properties

Molecular Weight:  184.18
Volume:  222.262
LogP:  4.473
LogD:  3.478
LogS:  -3.781
# Rotatable Bonds:  9
TPSA:  17.07
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.391
Synthetic Accessibility Score:  2.53
Fsp3:  0.917
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  2
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.542
MDCK Permeability:  1.5009339222160634e-05
Pgp-inhibitor:  0.008
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.99
30% Bioavailability (F30%):  0.994

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.994
Plasma Protein Binding (PPB):  74.80448913574219%
Volume Distribution (VD):  3.841
Pgp-substrate:  18.41066551208496%

ADMET: Metabolism

CYP1A2-inhibitor:  0.665
CYP1A2-substrate:  0.603
CYP2C19-inhibitor:  0.287
CYP2C19-substrate:  0.373
CYP2C9-inhibitor:  0.214
CYP2C9-substrate:  0.822
CYP2D6-inhibitor:  0.176
CYP2D6-substrate:  0.241
CYP3A4-inhibitor:  0.331
CYP3A4-substrate:  0.137

ADMET: Excretion

Clearance (CL):  5.935
Half-life (T1/2):  0.431

ADMET: Toxicity

hERG Blockers:  0.21
Human Hepatotoxicity (H-HT):  0.014
Drug-inuced Liver Injury (DILI):  0.123
AMES Toxicity:  0.013
Rat Oral Acute Toxicity:  0.013
Maximum Recommended Daily Dose:  0.023
Skin Sensitization:  0.973
Carcinogencity:  0.077
Eye Corrosion:  0.994
Eye Irritation:  0.984
Respiratory Toxicity:  0.896

Download Data

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

  Natural Product: NPC69245

Natural Product ID:  NPC69245
Common Name*:   2-Methylundecanal
IUPAC Name:   2-methylundecanal
Synonyms:  
Standard InCHIKey:  NFAVNWJJYQAGNB-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C12H24O/c1-3-4-5-6-7-8-9-10-12(2)11-13/h11-12H,3-10H2,1-2H3
SMILES:  CCCCCCCCCC(C=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3182849
PubChem CID:   61031
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
NPO26429 Capsella bursa-pastoris Species Brassicaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26429 Capsella bursa-pastoris Species Brassicaceae 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]
NPO26429 Capsella bursa-pastoris Species Brassicaceae 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
NPT153 Individual Protein Androgen Receptor Homo sapiens Potency n.a. 19496.2 nM PubChem BioAssay data set
NPT106 Individual Protein Peroxisome proliferator-activated receptor delta Homo sapiens Potency n.a. 54947.7 nM PubChem BioAssay data set
NPT162 Individual Protein Heat shock protein beta-1 Homo sapiens Potency n.a. 61652.4 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 24544.2 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 38570.8 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 19496.2 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 68589.6 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 17376 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 30899.4 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 43646.5 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 54482.7 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 43277.1 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 NPC69245 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 NPC218357
0.8529 High Similarity NPC179831
0.8529 High Similarity NPC254713
0.8529 High Similarity NPC262505
0.8529 High Similarity NPC49151
0.8529 High Similarity NPC261991
0.8056 Intermediate Similarity NPC49615
0.7727 Intermediate Similarity NPC13105
0.7692 Intermediate Similarity NPC223315
0.7647 Intermediate Similarity NPC287782
0.7647 Intermediate Similarity NPC32279
0.7632 Intermediate Similarity NPC301919
0.7317 Intermediate Similarity NPC135077
0.7317 Intermediate Similarity NPC215118
0.7317 Intermediate Similarity NPC59570
0.7317 Intermediate Similarity NPC45270
0.7222 Intermediate Similarity NPC321646
0.7073 Intermediate Similarity NPC141634
0.7059 Intermediate Similarity NPC59581
0.6977 Remote Similarity NPC18397
0.6944 Remote Similarity NPC222997
0.6944 Remote Similarity NPC42403
0.6944 Remote Similarity NPC79887
0.6944 Remote Similarity NPC221192
0.6944 Remote Similarity NPC29561
0.6944 Remote Similarity NPC153439
0.6944 Remote Similarity NPC196434
0.6944 Remote Similarity NPC4962
0.6765 Remote Similarity NPC304927
0.6765 Remote Similarity NPC289974
0.6757 Remote Similarity NPC168982
0.6735 Remote Similarity NPC22182
0.6667 Remote Similarity NPC198118
0.6667 Remote Similarity NPC305182
0.6667 Remote Similarity NPC55023
0.6667 Remote Similarity NPC38859
0.6667 Remote Similarity NPC295442
0.6579 Remote Similarity NPC149101
0.6579 Remote Similarity NPC16578
0.6579 Remote Similarity NPC76608
0.6579 Remote Similarity NPC225318
0.6579 Remote Similarity NPC268596
0.6531 Remote Similarity NPC314084
0.6522 Remote Similarity NPC314679
0.6512 Remote Similarity NPC48930
0.6471 Remote Similarity NPC250539
0.6471 Remote Similarity NPC164646
0.6444 Remote Similarity NPC171783
0.6389 Remote Similarity NPC100997
0.6383 Remote Similarity NPC83187
0.6383 Remote Similarity NPC21844
0.6383 Remote Similarity NPC98246
0.6383 Remote Similarity NPC173996
0.6383 Remote Similarity NPC131981
0.6383 Remote Similarity NPC22098
0.6383 Remote Similarity NPC249754
0.6383 Remote Similarity NPC40249
0.6383 Remote Similarity NPC285814
0.6383 Remote Similarity NPC195246
0.6383 Remote Similarity NPC276009
0.6346 Remote Similarity NPC188789
0.625 Remote Similarity NPC324793
0.625 Remote Similarity NPC294440
0.625 Remote Similarity NPC477878
0.6176 Remote Similarity NPC133819
0.617 Remote Similarity NPC308301
0.617 Remote Similarity NPC239754
0.6136 Remote Similarity NPC149299
0.6136 Remote Similarity NPC40597
0.6136 Remote Similarity NPC250028
0.6136 Remote Similarity NPC256163
0.6122 Remote Similarity NPC247786
0.6122 Remote Similarity NPC258672
0.6122 Remote Similarity NPC293343
0.6087 Remote Similarity NPC106819
0.6053 Remote Similarity NPC158107
0.6047 Remote Similarity NPC54980
0.6047 Remote Similarity NPC201622
0.6047 Remote Similarity NPC305660
0.6047 Remote Similarity NPC22903
0.6042 Remote Similarity NPC163751
0.6042 Remote Similarity NPC44363
0.6042 Remote Similarity NPC110234
0.6 Remote Similarity NPC248763
0.6 Remote Similarity NPC325452
0.6 Remote Similarity NPC53541
0.5918 Remote Similarity NPC20017
0.5909 Remote Similarity NPC81263
0.5909 Remote Similarity NPC219536
0.5909 Remote Similarity NPC3531
0.5909 Remote Similarity NPC31551
0.5909 Remote Similarity NPC223249
0.5909 Remote Similarity NPC80234
0.5882 Remote Similarity NPC274182
0.5882 Remote Similarity NPC37479
0.5882 Remote Similarity NPC236623
0.5882 Remote Similarity NPC234829
0.587 Remote Similarity NPC236579
0.587 Remote Similarity NPC203531
0.5854 Remote Similarity NPC248190
0.5849 Remote Similarity NPC100809
0.5849 Remote Similarity NPC209431
0.5849 Remote Similarity NPC319589
0.5833 Remote Similarity NPC66624
0.5833 Remote Similarity NPC307594
0.5833 Remote Similarity NPC282440
0.5814 Remote Similarity NPC14608
0.5814 Remote Similarity NPC177022
0.5778 Remote Similarity NPC161097
0.5778 Remote Similarity NPC28598
0.5778 Remote Similarity NPC165533
0.5745 Remote Similarity NPC76051
0.5714 Remote Similarity NPC121215
0.5714 Remote Similarity NPC156630
0.5686 Remote Similarity NPC116906
0.5682 Remote Similarity NPC316546
0.5676 Remote Similarity NPC79591
0.5667 Remote Similarity NPC268039
0.566 Remote Similarity NPC474141
0.566 Remote Similarity NPC72722
0.5625 Remote Similarity NPC47363
0.5625 Remote Similarity NPC287231
0.5625 Remote Similarity NPC469781
0.5614 Remote Similarity NPC470363
0.5614 Remote Similarity NPC472020
0.5614 Remote Similarity NPC475821
0.5614 Remote Similarity NPC226602
0.5614 Remote Similarity NPC472019
0.561 Remote Similarity NPC178643
0.561 Remote Similarity NPC41007
0.561 Remote Similarity NPC168714
0.561 Remote Similarity NPC35371

  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 NPC69245 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
0.6591 Remote Similarity NPD387 Clinical (unspecified phase)
0.6522 Remote Similarity NPD634 Phase 3
0.6383 Remote Similarity NPD344 Approved
0.6383 Remote Similarity NPD345 Approved
0.6383 Remote Similarity NPD343 Approved
0.619 Remote Similarity NPD9449 Clinical (unspecified phase)
0.6098 Remote Similarity NPD9447 Approved
0.5909 Remote Similarity NPD77 Approved
0.5909 Remote Similarity NPD9450 Approved
0.5849 Remote Similarity NPD3729 Clinical (unspecified phase)
0.5769 Remote Similarity NPD3186 Phase 1
0.5682 Remote Similarity NPD3206 Approved
0.5625 Remote Similarity NPD2699 Approved
0.5614 Remote Similarity NPD3198 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