Structure

Physi-Chem Properties

Molecular Weight:  258.18
Volume:  280.588
LogP:  3.672
LogD:  3.251
LogS:  -3.441
# Rotatable Bonds:  13
TPSA:  52.6
# H-Bond Aceptor:  4
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.422
Synthetic Accessibility Score:  1.77
Fsp3:  0.857
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:  -4.547
MDCK Permeability:  3.442060551606119e-05
Pgp-inhibitor:  0.993
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.002
20% Bioavailability (F20%):  0.906
30% Bioavailability (F30%):  0.976

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.542
Plasma Protein Binding (PPB):  88.85566711425781%
Volume Distribution (VD):  0.409
Pgp-substrate:  10.063037872314453%

ADMET: Metabolism

CYP1A2-inhibitor:  0.976
CYP1A2-substrate:  0.262
CYP2C19-inhibitor:  0.846
CYP2C19-substrate:  0.094
CYP2C9-inhibitor:  0.841
CYP2C9-substrate:  0.762
CYP2D6-inhibitor:  0.095
CYP2D6-substrate:  0.071
CYP3A4-inhibitor:  0.413
CYP3A4-substrate:  0.19

ADMET: Excretion

Clearance (CL):  8.937
Half-life (T1/2):  0.81

ADMET: Toxicity

hERG Blockers:  0.144
Human Hepatotoxicity (H-HT):  0.014
Drug-inuced Liver Injury (DILI):  0.186
AMES Toxicity:  0.008
Rat Oral Acute Toxicity:  0.011
Maximum Recommended Daily Dose:  0.018
Skin Sensitization:  0.946
Carcinogencity:  0.171
Eye Corrosion:  0.964
Eye Irritation:  0.948
Respiratory Toxicity:  0.055

Download Data

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

  Natural Product: NPC53541

Natural Product ID:  NPC53541
Common Name*:   Diethyl Decanedioate
IUPAC Name:   diethyl decanedioate
Synonyms:  
Standard InCHIKey:  ONKUXPIBXRRIDU-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C14H26O4/c1-3-17-13(15)11-9-7-5-6-8-10-12-14(16)18-4-2/h3-12H2,1-2H3
SMILES:  CCOC(=O)CCCCCCCCC(=O)OCC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1884461
PubChem CID:   8049
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
NPO10680 Cistanche deserticola Species Orobanchaceae Eukaryota n.a. n.a. n.a. PMID[25900014]
NPO10680 Cistanche deserticola Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10680 Cistanche deserticola Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO10680 Cistanche deserticola Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO10680 Cistanche deserticola Species Orobanchaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO10680 Cistanche deserticola Species Orobanchaceae 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
NPT198 Individual Protein Vitamin D receptor Homo sapiens Potency n.a. 100000.0 nM PMID[572183]
NPT2 Others Unspecified Potency n.a. 68589.6 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 61130.6 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 48557.7 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 54482.7 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 NPC53541 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
0.9737 High Similarity NPC40597
0.9737 High Similarity NPC250028
0.9737 High Similarity NPC149299
0.9737 High Similarity NPC256163
0.9474 High Similarity NPC223249
0.9474 High Similarity NPC31551
0.9474 High Similarity NPC219536
0.9474 High Similarity NPC80234
0.925 High Similarity NPC236579
0.925 High Similarity NPC203531
0.9231 High Similarity NPC165533
0.9211 High Similarity NPC201622
0.9211 High Similarity NPC54980
0.9211 High Similarity NPC22903
0.9211 High Similarity NPC305660
0.881 High Similarity NPC47363
0.881 High Similarity NPC287231
0.875 High Similarity NPC28598
0.875 High Similarity NPC12156
0.875 High Similarity NPC161097
0.8684 High Similarity NPC80641
0.8684 High Similarity NPC80396
0.8684 High Similarity NPC154642
0.8605 High Similarity NPC63182
0.8605 High Similarity NPC52700
0.8605 High Similarity NPC105329
0.8605 High Similarity NPC145045
0.85 High Similarity NPC81263
0.8421 Intermediate Similarity NPC156630
0.8421 Intermediate Similarity NPC301398
0.8421 Intermediate Similarity NPC223374
0.8421 Intermediate Similarity NPC86545
0.8421 Intermediate Similarity NPC196442
0.8409 Intermediate Similarity NPC326957
0.8372 Intermediate Similarity NPC273545
0.8261 Intermediate Similarity NPC55678
0.8182 Intermediate Similarity NPC12438
0.8182 Intermediate Similarity NPC30195
0.8158 Intermediate Similarity NPC286498
0.8158 Intermediate Similarity NPC154396
0.8158 Intermediate Similarity NPC57499
0.814 Intermediate Similarity NPC317128
0.8085 Intermediate Similarity NPC287811
0.8049 Intermediate Similarity NPC113928
0.8049 Intermediate Similarity NPC294085
0.8049 Intermediate Similarity NPC279026
0.8049 Intermediate Similarity NPC201844
0.8049 Intermediate Similarity NPC154186
0.8049 Intermediate Similarity NPC183424
0.8049 Intermediate Similarity NPC301585
0.8049 Intermediate Similarity NPC301696
0.8049 Intermediate Similarity NPC214610
0.8049 Intermediate Similarity NPC14227
0.8049 Intermediate Similarity NPC261080
0.8049 Intermediate Similarity NPC118968
0.8043 Intermediate Similarity NPC26253
0.8 Intermediate Similarity NPC249754
0.8 Intermediate Similarity NPC128996
0.7907 Intermediate Similarity NPC176500
0.7895 Intermediate Similarity NPC286695
0.7895 Intermediate Similarity NPC322892
0.7872 Intermediate Similarity NPC305182
0.7826 Intermediate Similarity NPC106872
0.7805 Intermediate Similarity NPC268826
0.7778 Intermediate Similarity NPC308301
0.7708 Intermediate Similarity NPC314084
0.7674 Intermediate Similarity NPC307783
0.7674 Intermediate Similarity NPC196924
0.7674 Intermediate Similarity NPC216630
0.7674 Intermediate Similarity NPC171736
0.7674 Intermediate Similarity NPC209970
0.7674 Intermediate Similarity NPC149184
0.766 Intermediate Similarity NPC250919
0.7632 Intermediate Similarity NPC12904
0.7632 Intermediate Similarity NPC40965
0.7609 Intermediate Similarity NPC324004
0.7609 Intermediate Similarity NPC328497
0.76 Intermediate Similarity NPC23155
0.76 Intermediate Similarity NPC320588
0.76 Intermediate Similarity NPC469937
0.76 Intermediate Similarity NPC53463
0.7561 Intermediate Similarity NPC14608
0.7551 Intermediate Similarity NPC310746
0.75 Intermediate Similarity NPC155872
0.75 Intermediate Similarity NPC67462
0.75 Intermediate Similarity NPC289344
0.7447 Intermediate Similarity NPC131770
0.7447 Intermediate Similarity NPC216130
0.7447 Intermediate Similarity NPC200618
0.7391 Intermediate Similarity NPC282440
0.7333 Intermediate Similarity NPC74845
0.7333 Intermediate Similarity NPC255837
0.7333 Intermediate Similarity NPC19305
0.7317 Intermediate Similarity NPC134782
0.7317 Intermediate Similarity NPC155263
0.7292 Intermediate Similarity NPC304162
0.7209 Intermediate Similarity NPC94368
0.7174 Intermediate Similarity NPC8219
0.7174 Intermediate Similarity NPC55023
0.7143 Intermediate Similarity NPC90904
0.7115 Intermediate Similarity NPC200845
0.7115 Intermediate Similarity NPC128061
0.7115 Intermediate Similarity NPC28779
0.7115 Intermediate Similarity NPC10316
0.7115 Intermediate Similarity NPC223677
0.7059 Intermediate Similarity NPC71761
0.7021 Intermediate Similarity NPC314679
0.7021 Intermediate Similarity NPC172042
0.7 Intermediate Similarity NPC147054
0.7 Intermediate Similarity NPC100096
0.6977 Remote Similarity NPC316546
0.6957 Remote Similarity NPC76051
0.6909 Remote Similarity NPC470363
0.6909 Remote Similarity NPC17935
0.6889 Remote Similarity NPC163746
0.6889 Remote Similarity NPC103286
0.6875 Remote Similarity NPC21844
0.6863 Remote Similarity NPC161366
0.6809 Remote Similarity NPC469781
0.6786 Remote Similarity NPC45097
0.675 Remote Similarity NPC261991
0.675 Remote Similarity NPC254713
0.675 Remote Similarity NPC262505
0.675 Remote Similarity NPC49151
0.675 Remote Similarity NPC179831
0.6739 Remote Similarity NPC289686
0.6739 Remote Similarity NPC71317
0.6739 Remote Similarity NPC301528
0.6739 Remote Similarity NPC129972
0.6735 Remote Similarity NPC13105
0.6735 Remote Similarity NPC477878
0.6735 Remote Similarity NPC68577
0.6735 Remote Similarity NPC324793
0.6731 Remote Similarity NPC39633
0.6731 Remote Similarity NPC139545
0.6731 Remote Similarity NPC309606
0.6667 Remote Similarity NPC317203
0.6607 Remote Similarity NPC472019
0.6607 Remote Similarity NPC226602
0.6607 Remote Similarity NPC472020
0.6604 Remote Similarity NPC319589
0.66 Remote Similarity NPC163345
0.66 Remote Similarity NPC223675
0.6591 Remote Similarity NPC73245
0.6585 Remote Similarity NPC99700
0.6585 Remote Similarity NPC35371
0.6585 Remote Similarity NPC108238
0.6585 Remote Similarity NPC168714
0.6585 Remote Similarity NPC178643
0.6585 Remote Similarity NPC328710
0.6585 Remote Similarity NPC18224
0.6585 Remote Similarity NPC175342
0.6585 Remote Similarity NPC41007
0.6579 Remote Similarity NPC143211
0.6579 Remote Similarity NPC248233
0.6552 Remote Similarity NPC54925
0.6522 Remote Similarity NPC248763
0.6522 Remote Similarity NPC325452
0.6512 Remote Similarity NPC321699
0.6512 Remote Similarity NPC301919
0.65 Remote Similarity NPC168982
0.6491 Remote Similarity NPC229252
0.6491 Remote Similarity NPC472021
0.6491 Remote Similarity NPC143857
0.6481 Remote Similarity NPC228473
0.6471 Remote Similarity NPC224227
0.6441 Remote Similarity NPC314103
0.6429 Remote Similarity NPC49615
0.6415 Remote Similarity NPC72722
0.64 Remote Similarity NPC180534
0.6379 Remote Similarity NPC306750
0.6346 Remote Similarity NPC262968
0.6346 Remote Similarity NPC470410
0.6346 Remote Similarity NPC470412
0.6341 Remote Similarity NPC272426
0.6333 Remote Similarity NPC322319
0.6333 Remote Similarity NPC326651
0.6333 Remote Similarity NPC325117
0.6333 Remote Similarity NPC469926
0.6327 Remote Similarity NPC166287
0.6316 Remote Similarity NPC166804
0.6316 Remote Similarity NPC475821
0.6275 Remote Similarity NPC207815
0.6271 Remote Similarity NPC235788
0.6271 Remote Similarity NPC325773
0.625 Remote Similarity NPC42403
0.625 Remote Similarity NPC79887
0.625 Remote Similarity NPC4962
0.625 Remote Similarity NPC196434
0.625 Remote Similarity NPC222997
0.625 Remote Similarity NPC29561
0.625 Remote Similarity NPC221192
0.625 Remote Similarity NPC153439
0.625 Remote Similarity NPC127696
0.623 Remote Similarity NPC315525
0.623 Remote Similarity NPC135043
0.6226 Remote Similarity NPC281245
0.6167 Remote Similarity NPC328089
0.6167 Remote Similarity NPC68343
0.6154 Remote Similarity NPC142103

  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 NPC53541 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
0.881 High Similarity NPD2699 Approved
0.825 Intermediate Similarity NPD3206 Approved
0.8222 Intermediate Similarity NPD6125 Clinical (unspecified phase)
0.8049 Intermediate Similarity NPD9448 Phase 2
0.8049 Intermediate Similarity NPD9655 Approved
0.8049 Intermediate Similarity NPD633 Phase 3
0.7674 Intermediate Similarity NPD2270 Approved
0.76 Intermediate Similarity NPD3728 Approved
0.76 Intermediate Similarity NPD3730 Approved
0.75 Intermediate Similarity NPD387 Clinical (unspecified phase)
0.7174 Intermediate Similarity NPD3199 Clinical (unspecified phase)
0.7083 Intermediate Similarity NPD2266 Phase 2
0.7021 Intermediate Similarity NPD634 Phase 3
0.6923 Remote Similarity NPD3729 Clinical (unspecified phase)
0.6829 Remote Similarity NPD900 Approved
0.6744 Remote Similarity NPD9449 Clinical (unspecified phase)
0.64 Remote Similarity NPD622 Approved
0.6346 Remote Similarity NPD28 Approved
0.6346 Remote Similarity NPD29 Approved
0.6341 Remote Similarity NPD908 Approved
0.6341 Remote Similarity NPD907 Approved
0.6341 Remote Similarity NPD1461 Approved
0.6327 Remote Similarity NPD9430 Approved
0.6327 Remote Similarity NPD9431 Approved
0.6279 Remote Similarity NPD9447 Approved
0.6226 Remote Similarity NPD3186 Phase 1
0.6111 Remote Similarity NPD3172 Approved
0.6087 Remote Similarity NPD77 Approved
0.6087 Remote Similarity NPD9450 Approved
0.6038 Remote Similarity NPD9638 Phase 2
0.6034 Remote Similarity NPD3198 Approved
0.6032 Remote Similarity NPD8278 Approved
0.6 Remote Similarity NPD3194 Approved
0.6 Remote Similarity NPD4266 Approved
0.6 Remote Similarity NPD3196 Approved
0.6 Remote Similarity NPD3195 Phase 2
0.6 Remote Similarity NPD615 Clinical (unspecified phase)
0.5957 Remote Similarity NPD7536 Approved
0.5938 Remote Similarity NPD8277 Approved
0.5902 Remote Similarity NPD7909 Approved
0.587 Remote Similarity NPD9513 Phase 1
0.5818 Remote Similarity NPD630 Approved
0.5818 Remote Similarity NPD631 Approved
0.5806 Remote Similarity NPD9496 Clinical (unspecified phase)
0.5781 Remote Similarity NPD229 Approved
0.5778 Remote Similarity NPD370 Phase 3
0.5769 Remote Similarity NPD5343 Approved
0.5758 Remote Similarity NPD2256 Clinical (unspecified phase)
0.5692 Remote Similarity NPD3725 Approved
0.5692 Remote Similarity NPD3726 Approved
0.569 Remote Similarity NPD4279 Approved
0.5686 Remote Similarity NPD3174 Discontinued
0.5645 Remote Similarity NPD3197 Phase 1

  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