Structure

Physi-Chem Properties

Molecular Weight:  174.09
Volume:  176.812
LogP:  0.841
LogD:  0.873
LogS:  -1.134
# Rotatable Bonds:  7
TPSA:  52.6
# H-Bond Aceptor:  4
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.459
Synthetic Accessibility Score:  1.698
Fsp3:  0.75
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:  -4.488
MDCK Permeability:  7.616171933477744e-05
Pgp-inhibitor:  0.802
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.006
30% Bioavailability (F30%):  0.975

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.986
Plasma Protein Binding (PPB):  22.132556915283203%
Volume Distribution (VD):  0.542
Pgp-substrate:  75.72518157958984%

ADMET: Metabolism

CYP1A2-inhibitor:  0.476
CYP1A2-substrate:  0.462
CYP2C19-inhibitor:  0.352
CYP2C19-substrate:  0.763
CYP2C9-inhibitor:  0.04
CYP2C9-substrate:  0.498
CYP2D6-inhibitor:  0.011
CYP2D6-substrate:  0.165
CYP3A4-inhibitor:  0.032
CYP3A4-substrate:  0.262

ADMET: Excretion

Clearance (CL):  9.382
Half-life (T1/2):  0.929

ADMET: Toxicity

hERG Blockers:  0.012
Human Hepatotoxicity (H-HT):  0.249
Drug-inuced Liver Injury (DILI):  0.223
AMES Toxicity:  0.013
Rat Oral Acute Toxicity:  0.008
Maximum Recommended Daily Dose:  0.095
Skin Sensitization:  0.57
Carcinogencity:  0.063
Eye Corrosion:  0.94
Eye Irritation:  0.73
Respiratory Toxicity:  0.04

Download Data

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

  Natural Product: NPC57499

Natural Product ID:  NPC57499
Common Name*:   Dimethyl Hexanedioate
IUPAC Name:   dimethyl hexanedioate
Synonyms:  
Standard InCHIKey:  UDSFAEKRVUSQDD-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C8H14O4/c1-11-7(9)5-3-4-6-8(10)12-2/h3-6H2,1-2H3
SMILES:  COC(=O)CCCCC(=O)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1566491
PubChem CID:   12329
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0000324] Fatty acid esters
          • [CHEMONTID:0003417] Fatty acid methyl 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
NPO9822 Typha angustifolia Species Typhaceae Eukaryota n.a. n.a. Database[FooDB]
NPO9822 Typha angustifolia Species Typhaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO2554 Biancaea sappan Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9822 Typha angustifolia Species Typhaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9822 Typha angustifolia Species Typhaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28251 Typha orientalis Species Typhaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO9822 Typha angustifolia Species Typhaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2554 Biancaea sappan Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2554 Biancaea sappan Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO9822 Typha angustifolia Species Typhaceae 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 = 79432.8 nM PMID[558622]
NPT249 Individual Protein Glucocorticoid receptor Homo sapiens Potency n.a. 6309.6 nM PMID[558622]
NPT539 Individual Protein Cellular tumor antigen p53 Homo sapiens Potency n.a. 1.6 nM PMID[558624]
NPT10 Individual Protein Geminin Homo sapiens Potency n.a. 461.1 nM PMID[558623]
NPT49 Individual Protein DNA-(apurinic or apyrimidinic site) lyase Homo sapiens Potency n.a. 9466.2 nM PMID[558623]
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens Potency n.a. 61503.8 nM PubChem BioAssay data set
NPT533 Protein-Protein Interaction Runt-related transcription factor 1/Core-binding factor subunit beta Homo sapiens Potency n.a. 8912.5 nM PMID[558622]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum Potency n.a. 14715.7 nM PMID[558623]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum Potency n.a. 2078.7 nM PMID[558623]
NPT2 Others Unspecified Potency n.a. 5.5 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 77428.6 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 5494.1 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 439.4 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 NPC57499 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
0.8824 High Similarity NPC154642
0.8824 High Similarity NPC80396
0.8611 High Similarity NPC31551
0.8611 High Similarity NPC81263
0.8611 High Similarity NPC219536
0.8333 Intermediate Similarity NPC201622
0.8333 Intermediate Similarity NPC22903
0.8333 Intermediate Similarity NPC54980
0.8333 Intermediate Similarity NPC305660
0.8235 Intermediate Similarity NPC154396
0.8158 Intermediate Similarity NPC53541
0.8108 Intermediate Similarity NPC80234
0.8 Intermediate Similarity NPC289344
0.8 Intermediate Similarity NPC156630
0.7941 Intermediate Similarity NPC286695
0.7941 Intermediate Similarity NPC328710
0.7941 Intermediate Similarity NPC175342
0.7941 Intermediate Similarity NPC18224
0.7941 Intermediate Similarity NPC322892
0.7895 Intermediate Similarity NPC149299
0.7895 Intermediate Similarity NPC250028
0.7895 Intermediate Similarity NPC28598
0.7895 Intermediate Similarity NPC256163
0.7895 Intermediate Similarity NPC40597
0.7895 Intermediate Similarity NPC161097
0.7778 Intermediate Similarity NPC80641
0.7647 Intermediate Similarity NPC12904
0.7647 Intermediate Similarity NPC40965
0.7632 Intermediate Similarity NPC223249
0.7632 Intermediate Similarity NPC94368
0.7568 Intermediate Similarity NPC14608
0.75 Intermediate Similarity NPC317203
0.75 Intermediate Similarity NPC203531
0.75 Intermediate Similarity NPC155872
0.75 Intermediate Similarity NPC236579
0.7436 Intermediate Similarity NPC12156
0.7436 Intermediate Similarity NPC165533
0.7419 Intermediate Similarity NPC28246
0.7381 Intermediate Similarity NPC308301
0.7368 Intermediate Similarity NPC73245
0.7368 Intermediate Similarity NPC268826
0.7297 Intermediate Similarity NPC134782
0.7297 Intermediate Similarity NPC155263
0.7222 Intermediate Similarity NPC286498
0.7209 Intermediate Similarity NPC249754
0.7179 Intermediate Similarity NPC301585
0.7179 Intermediate Similarity NPC183424
0.7179 Intermediate Similarity NPC261080
0.7179 Intermediate Similarity NPC113928
0.7179 Intermediate Similarity NPC279026
0.7179 Intermediate Similarity NPC294085
0.7179 Intermediate Similarity NPC118968
0.7179 Intermediate Similarity NPC214610
0.7179 Intermediate Similarity NPC301696
0.7179 Intermediate Similarity NPC201844
0.7179 Intermediate Similarity NPC154186
0.7179 Intermediate Similarity NPC14227
0.7143 Intermediate Similarity NPC287231
0.7143 Intermediate Similarity NPC47363
0.7143 Intermediate Similarity NPC273545
0.7105 Intermediate Similarity NPC109026
0.7105 Intermediate Similarity NPC206924
0.7105 Intermediate Similarity NPC252843
0.7073 Intermediate Similarity NPC176500
0.7059 Intermediate Similarity NPC174368
0.7059 Intermediate Similarity NPC180423
0.7027 Intermediate Similarity NPC196442
0.7027 Intermediate Similarity NPC301398
0.7027 Intermediate Similarity NPC86545
0.7027 Intermediate Similarity NPC223374
0.6977 Remote Similarity NPC30195
0.6977 Remote Similarity NPC52700
0.6977 Remote Similarity NPC105329
0.6977 Remote Similarity NPC145045
0.6977 Remote Similarity NPC12438
0.6977 Remote Similarity NPC282440
0.6977 Remote Similarity NPC172042
0.6977 Remote Similarity NPC63182
0.697 Remote Similarity NPC143211
0.697 Remote Similarity NPC248233
0.6944 Remote Similarity NPC108238
0.6944 Remote Similarity NPC99700
0.6905 Remote Similarity NPC317128
0.6842 Remote Similarity NPC321699
0.6829 Remote Similarity NPC149184
0.6829 Remote Similarity NPC171736
0.6829 Remote Similarity NPC216630
0.6829 Remote Similarity NPC325452
0.6829 Remote Similarity NPC103286
0.6829 Remote Similarity NPC209970
0.6829 Remote Similarity NPC307783
0.6829 Remote Similarity NPC248763
0.6829 Remote Similarity NPC196924
0.6829 Remote Similarity NPC163746
0.6818 Remote Similarity NPC326957
0.6774 Remote Similarity NPC8187
0.6765 Remote Similarity NPC159398
0.6739 Remote Similarity NPC55678
0.6667 Remote Similarity NPC158179
0.6667 Remote Similarity NPC106872
0.6667 Remote Similarity NPC289686
0.6667 Remote Similarity NPC71317
0.6667 Remote Similarity NPC301528
0.6667 Remote Similarity NPC129972
0.6667 Remote Similarity NPC128996
0.6667 Remote Similarity NPC216130
0.6667 Remote Similarity NPC67462
0.6667 Remote Similarity NPC166804
0.6596 Remote Similarity NPC287811
0.6571 Remote Similarity NPC248139
0.6522 Remote Similarity NPC250919
0.6522 Remote Similarity NPC163345
0.6522 Remote Similarity NPC26253
0.6512 Remote Similarity NPC74845
0.6512 Remote Similarity NPC255837
0.6512 Remote Similarity NPC19305
0.65 Remote Similarity NPC316546
0.6486 Remote Similarity NPC41007
0.6486 Remote Similarity NPC178643
0.6486 Remote Similarity NPC168714
0.6486 Remote Similarity NPC125575
0.6486 Remote Similarity NPC35371
0.6486 Remote Similarity NPC147054
0.6444 Remote Similarity NPC328497
0.6444 Remote Similarity NPC324004
0.6389 Remote Similarity NPC21374
0.6389 Remote Similarity NPC302611
0.6383 Remote Similarity NPC305182
0.6364 Remote Similarity NPC41485
0.6364 Remote Similarity NPC8219
0.6364 Remote Similarity NPC3693
0.6364 Remote Similarity NPC55023
0.6364 Remote Similarity NPC32280
0.6341 Remote Similarity NPC3531
0.6316 Remote Similarity NPC7814
0.6316 Remote Similarity NPC127142
0.6304 Remote Similarity NPC200618
0.6304 Remote Similarity NPC131770
0.6286 Remote Similarity NPC55956
0.625 Remote Similarity NPC314084
0.625 Remote Similarity NPC203105
0.6222 Remote Similarity NPC314679
0.62 Remote Similarity NPC469937
0.62 Remote Similarity NPC320588
0.62 Remote Similarity NPC53463
0.62 Remote Similarity NPC23155
0.6176 Remote Similarity NPC211250
0.6176 Remote Similarity NPC149209
0.6176 Remote Similarity NPC59581
0.6176 Remote Similarity NPC79591
0.617 Remote Similarity NPC304162
0.6122 Remote Similarity NPC310746
0.6122 Remote Similarity NPC216407
0.6122 Remote Similarity NPC161366
0.6111 Remote Similarity NPC127696
0.6098 Remote Similarity NPC325454
0.6087 Remote Similarity NPC21844
0.6061 Remote Similarity NPC30338
0.6061 Remote Similarity NPC110107
0.6042 Remote Similarity NPC90904
0.6 Remote Similarity NPC309606
0.6 Remote Similarity NPC139545
0.6 Remote Similarity NPC39633
0.6 Remote Similarity NPC312547
0.5962 Remote Similarity NPC473936
0.5957 Remote Similarity NPC324793
0.5957 Remote Similarity NPC477878
0.5946 Remote Similarity NPC168982
0.5946 Remote Similarity NPC265882
0.5918 Remote Similarity NPC100096
0.5918 Remote Similarity NPC470411
0.5909 Remote Similarity NPC325102
0.5897 Remote Similarity NPC140229
0.5882 Remote Similarity NPC66624
0.5882 Remote Similarity NPC319589
0.587 Remote Similarity NPC166287
0.5854 Remote Similarity NPC317945
0.5833 Remote Similarity NPC149821
0.5833 Remote Similarity NPC295442
0.5833 Remote Similarity NPC32279
0.5833 Remote Similarity NPC476469
0.5833 Remote Similarity NPC281943
0.5833 Remote Similarity NPC5413
0.5833 Remote Similarity NPC234005
0.5833 Remote Similarity NPC317739
0.5789 Remote Similarity NPC49151
0.5789 Remote Similarity NPC254713
0.5789 Remote Similarity NPC262505
0.5789 Remote Similarity NPC261991
0.5789 Remote Similarity NPC179831
0.5789 Remote Similarity NPC281883
0.5789 Remote Similarity NPC280532
0.5778 Remote Similarity NPC76051
0.5778 Remote Similarity NPC323974
0.5769 Remote Similarity NPC128061
0.5769 Remote Similarity NPC200845
0.5769 Remote Similarity NPC28779
0.5769 Remote Similarity NPC10316
0.5769 Remote Similarity NPC228473
0.5769 Remote Similarity NPC223677

  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 NPC57499 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
0.7568 Intermediate Similarity NPD9449 Clinical (unspecified phase)
0.7368 Intermediate Similarity NPD3206 Approved
0.7179 Intermediate Similarity NPD9655 Approved
0.7179 Intermediate Similarity NPD633 Phase 3
0.7179 Intermediate Similarity NPD9448 Phase 2
0.7143 Intermediate Similarity NPD2699 Approved
0.7045 Intermediate Similarity NPD6125 Clinical (unspecified phase)
0.7045 Intermediate Similarity NPD2266 Phase 2
0.7027 Intermediate Similarity NPD9447 Approved
0.6829 Remote Similarity NPD2270 Approved
0.6757 Remote Similarity NPD900 Approved
0.6667 Remote Similarity NPD387 Clinical (unspecified phase)
0.6571 Remote Similarity NPD62 Approved
0.6452 Remote Similarity NPD8615 Phase 2
0.6452 Remote Similarity NPD8616 Clinical (unspecified phase)
0.6364 Remote Similarity NPD3199 Clinical (unspecified phase)
0.6341 Remote Similarity NPD9450 Approved
0.6341 Remote Similarity NPD77 Approved
0.6316 Remote Similarity NPD8857 Approved
0.6222 Remote Similarity NPD634 Phase 3
0.6222 Remote Similarity NPD3174 Discontinued
0.62 Remote Similarity NPD3730 Approved
0.62 Remote Similarity NPD3728 Approved
0.619 Remote Similarity NPD9635 Discontinued
0.6 Remote Similarity NPD370 Phase 3
0.6 Remote Similarity NPD8990 Clinical (unspecified phase)
0.5918 Remote Similarity NPD9638 Phase 2
0.5882 Remote Similarity NPD8592 Approved
0.5882 Remote Similarity NPD8591 Approved
0.5882 Remote Similarity NPD3729 Clinical (unspecified phase)
0.587 Remote Similarity NPD9431 Approved
0.587 Remote Similarity NPD9430 Approved
0.5833 Remote Similarity NPD3173 Approved
0.5789 Remote Similarity NPD9636 Phase 2
0.5778 Remote Similarity NPD9019 Approved
0.5714 Remote Similarity NPD8989 Approved
0.5686 Remote Similarity NPD630 Approved
0.5686 Remote Similarity NPD631 Approved
0.5625 Remote Similarity NPD5343 Approved
0.5625 Remote Similarity NPD622 Approved
0.56 Remote Similarity NPD28 Approved
0.56 Remote Similarity NPD29 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