Structure

Physi-Chem Properties

Molecular Weight:  216.14
Volume:  228.7
LogP:  2.405
LogD:  2.078
LogS:  -2.311
# Rotatable Bonds:  10
TPSA:  52.6
# H-Bond Aceptor:  4
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.46
Synthetic Accessibility Score:  1.74
Fsp3:  0.818
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.551
MDCK Permeability:  3.37E-05
Pgp-inhibitor:  0.985
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.034
30% Bioavailability (F30%):  0.967

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.991
Plasma Protein Binding (PPB):  54.52%
Volume Distribution (VD):  0.615
Pgp-substrate:  55.64%

ADMET: Metabolism

CYP1A2-inhibitor:  0.925
CYP1A2-substrate:  0.555
CYP2C19-inhibitor:  0.727
CYP2C19-substrate:  0.726
CYP2C9-inhibitor:  0.371
CYP2C9-substrate:  0.784
CYP2D6-inhibitor:  0.012
CYP2D6-substrate:  0.112
CYP3A4-inhibitor:  0.173
CYP3A4-substrate:  0.188

ADMET: Excretion

Clearance (CL):  9.464
Half-life (T1/2):  0.898

ADMET: Toxicity

hERG Blockers:  0.018
Human Hepatotoxicity (H-HT):  0.121
Drug-inuced Liver Injury (DILI):  0.209
AMES Toxicity:  0.011
Rat Oral Acute Toxicity:  0.01
Maximum Recommended Daily Dose:  0.071
Skin Sensitization:  0.864
Carcinogencity:  0.098
Eye Corrosion:  0.937
Eye Irritation:  0.704
Respiratory Toxicity:  0.088

Download Data

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

  Natural Product: NPC31551

Natural Product ID:  NPC31551
Common Name*:   Dimethyl Nonanedioate
IUPAC Name:   dimethyl nonanedioate
Synonyms:  
Standard InCHIKey:  DRUKNYVQGHETPO-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C11H20O4/c1-14-10(12)8-6-4-3-5-7-9-11(13)15-2/h3-9H2,1-2H3
SMILES:  COC(=O)CCCCCCCC(=O)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3188858
PubChem CID:   15612
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
NPO15462 Angelica sinensis Species Apiaceae Eukaryota roots purchased from Kiu Shun Trading Ltd., Vancouver, Canada 2000 PMID[16643021]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[25538068]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. PMID[27400088]
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]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1983 Fructus anisi stellati n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO9822 Typha angustifolia Species Typhaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO9822 Typha angustifolia Species Typhaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO15462 Angelica sinensis Species Apiaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
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]
NPO9822 Typha angustifolia Species Typhaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO15462 Angelica sinensis Species Apiaceae 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
NPT152 Individual Protein Nuclear factor erythroid 2-related factor 2 Homo sapiens Potency n.a. 21689.9 nM PubChem BioAssay data set
NPT162 Individual Protein Heat shock protein beta-1 Homo sapiens Potency n.a. 24541.2 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 21872.4 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 61130.6 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 68589.6 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 48557.7 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 NPC31551 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
1.0 High Similarity NPC219536
0.9722 High Similarity NPC305660
0.9722 High Similarity NPC54980
0.9722 High Similarity NPC201622
0.9722 High Similarity NPC22903
0.9474 High Similarity NPC53541
0.9211 High Similarity NPC256163
0.9211 High Similarity NPC161097
0.9211 High Similarity NPC250028
0.9211 High Similarity NPC40597
0.9211 High Similarity NPC28598
0.9211 High Similarity NPC149299
0.8947 High Similarity NPC80234
0.8947 High Similarity NPC223249
0.8889 High Similarity NPC156630
0.875 High Similarity NPC236579
0.875 High Similarity NPC203531
0.8718 High Similarity NPC165533
0.8718 High Similarity NPC12156
0.8611 High Similarity NPC57499
0.8462 Intermediate Similarity NPC214610
0.8462 Intermediate Similarity NPC154186
0.8462 Intermediate Similarity NPC301585
0.8462 Intermediate Similarity NPC183424
0.8462 Intermediate Similarity NPC118968
0.8462 Intermediate Similarity NPC14227
0.8462 Intermediate Similarity NPC113928
0.8462 Intermediate Similarity NPC301696
0.8462 Intermediate Similarity NPC201844
0.8462 Intermediate Similarity NPC261080
0.8462 Intermediate Similarity NPC294085
0.8462 Intermediate Similarity NPC279026
0.8333 Intermediate Similarity NPC47363
0.8333 Intermediate Similarity NPC287231
0.8205 Intermediate Similarity NPC268826
0.8158 Intermediate Similarity NPC80396
0.8158 Intermediate Similarity NPC80641
0.8158 Intermediate Similarity NPC154642
0.814 Intermediate Similarity NPC12438
0.814 Intermediate Similarity NPC105329
0.814 Intermediate Similarity NPC63182
0.814 Intermediate Similarity NPC145045
0.814 Intermediate Similarity NPC52700
0.814 Intermediate Similarity NPC30195
0.8095 Intermediate Similarity NPC317128
0.8049 Intermediate Similarity NPC307783
0.8049 Intermediate Similarity NPC196924
0.8049 Intermediate Similarity NPC216630
0.8049 Intermediate Similarity NPC209970
0.8049 Intermediate Similarity NPC171736
0.8049 Intermediate Similarity NPC149184
0.8 Intermediate Similarity NPC81263
0.7955 Intermediate Similarity NPC326957
0.7907 Intermediate Similarity NPC273545
0.7895 Intermediate Similarity NPC196442
0.7895 Intermediate Similarity NPC223374
0.7895 Intermediate Similarity NPC86545
0.7895 Intermediate Similarity NPC301398
0.7857 Intermediate Similarity NPC67462
0.7826 Intermediate Similarity NPC55678
0.7778 Intermediate Similarity NPC216130
0.7778 Intermediate Similarity NPC106872
0.7692 Intermediate Similarity NPC134782
0.7692 Intermediate Similarity NPC155263
0.7674 Intermediate Similarity NPC74845
0.7674 Intermediate Similarity NPC255837
0.7674 Intermediate Similarity NPC19305
0.766 Intermediate Similarity NPC287811
0.7632 Intermediate Similarity NPC154396
0.7632 Intermediate Similarity NPC286498
0.7609 Intermediate Similarity NPC26253
0.7556 Intermediate Similarity NPC249754
0.7556 Intermediate Similarity NPC324004
0.7556 Intermediate Similarity NPC328497
0.75 Intermediate Similarity NPC128996
0.75 Intermediate Similarity NPC8219
0.75 Intermediate Similarity NPC55023
0.7447 Intermediate Similarity NPC305182
0.7442 Intermediate Similarity NPC176500
0.7391 Intermediate Similarity NPC200618
0.7391 Intermediate Similarity NPC131770
0.7368 Intermediate Similarity NPC286695
0.7368 Intermediate Similarity NPC322892
0.7333 Intermediate Similarity NPC314679
0.7333 Intermediate Similarity NPC308301
0.7292 Intermediate Similarity NPC314084
0.7234 Intermediate Similarity NPC250919
0.7234 Intermediate Similarity NPC304162
0.7209 Intermediate Similarity NPC163746
0.7209 Intermediate Similarity NPC103286
0.72 Intermediate Similarity NPC320588
0.72 Intermediate Similarity NPC469937
0.72 Intermediate Similarity NPC53463
0.72 Intermediate Similarity NPC23155
0.7174 Intermediate Similarity NPC21844
0.7143 Intermediate Similarity NPC310746
0.7143 Intermediate Similarity NPC161366
0.7105 Intermediate Similarity NPC12904
0.7105 Intermediate Similarity NPC40965
0.7083 Intermediate Similarity NPC90904
0.7073 Intermediate Similarity NPC14608
0.7045 Intermediate Similarity NPC129972
0.7045 Intermediate Similarity NPC71317
0.7045 Intermediate Similarity NPC289686
0.7045 Intermediate Similarity NPC301528
0.7021 Intermediate Similarity NPC477878
0.7021 Intermediate Similarity NPC324793
0.7 Intermediate Similarity NPC139545
0.7 Intermediate Similarity NPC289344
0.7 Intermediate Similarity NPC39633
0.7 Intermediate Similarity NPC155872
0.7 Intermediate Similarity NPC309606
0.6957 Remote Similarity NPC282440
0.6939 Remote Similarity NPC100096
0.6923 Remote Similarity NPC328710
0.6923 Remote Similarity NPC18224
0.6923 Remote Similarity NPC175342
0.6923 Remote Similarity NPC147054
0.6905 Remote Similarity NPC73245
0.6889 Remote Similarity NPC76051
0.6863 Remote Similarity NPC319589
0.6842 Remote Similarity NPC168982
0.6818 Remote Similarity NPC248763
0.6818 Remote Similarity NPC325452
0.6744 Remote Similarity NPC94368
0.6739 Remote Similarity NPC469781
0.6735 Remote Similarity NPC224227
0.6731 Remote Similarity NPC200845
0.6731 Remote Similarity NPC228473
0.6731 Remote Similarity NPC10316
0.6731 Remote Similarity NPC223677
0.6731 Remote Similarity NPC28779
0.6731 Remote Similarity NPC128061
0.6667 Remote Similarity NPC13105
0.6667 Remote Similarity NPC49151
0.6667 Remote Similarity NPC180534
0.6667 Remote Similarity NPC261991
0.6667 Remote Similarity NPC72722
0.6667 Remote Similarity NPC254713
0.6667 Remote Similarity NPC262505
0.6667 Remote Similarity NPC71761
0.6667 Remote Similarity NPC179831
0.66 Remote Similarity NPC262968
0.66 Remote Similarity NPC470410
0.66 Remote Similarity NPC470412
0.6596 Remote Similarity NPC166287
0.6596 Remote Similarity NPC172042
0.6585 Remote Similarity NPC317203
0.6579 Remote Similarity NPC4962
0.6579 Remote Similarity NPC222997
0.6579 Remote Similarity NPC196434
0.6579 Remote Similarity NPC42403
0.6579 Remote Similarity NPC79887
0.6579 Remote Similarity NPC153439
0.6579 Remote Similarity NPC221192
0.6579 Remote Similarity NPC29561
0.6545 Remote Similarity NPC470363
0.6545 Remote Similarity NPC472020
0.6545 Remote Similarity NPC472019
0.6545 Remote Similarity NPC226602
0.6545 Remote Similarity NPC17935
0.6512 Remote Similarity NPC316546
0.6471 Remote Similarity NPC281245
0.6429 Remote Similarity NPC472021
0.6429 Remote Similarity NPC45097
0.6429 Remote Similarity NPC301919
0.64 Remote Similarity NPC50457
0.6389 Remote Similarity NPC28246
0.6364 Remote Similarity NPC3531
0.6346 Remote Similarity NPC1813
0.6346 Remote Similarity NPC139029
0.6346 Remote Similarity NPC36061
0.6346 Remote Similarity NPC294548
0.6341 Remote Similarity NPC49615
0.6327 Remote Similarity NPC68577
0.6316 Remote Similarity NPC469922
0.6316 Remote Similarity NPC469923
0.6316 Remote Similarity NPC198118
0.6316 Remote Similarity NPC38859
0.6316 Remote Similarity NPC295442
0.6279 Remote Similarity NPC158179
0.6279 Remote Similarity NPC206924
0.6279 Remote Similarity NPC109026
0.6279 Remote Similarity NPC252843
0.625 Remote Similarity NPC149101
0.625 Remote Similarity NPC268596
0.625 Remote Similarity NPC225318
0.625 Remote Similarity NPC272426
0.625 Remote Similarity NPC475821
0.625 Remote Similarity NPC16578
0.625 Remote Similarity NPC76608
0.6226 Remote Similarity NPC32467
0.6226 Remote Similarity NPC88966
0.6226 Remote Similarity NPC87394
0.6226 Remote Similarity NPC290563
0.6226 Remote Similarity NPC154245
0.6226 Remote Similarity NPC424
0.6226 Remote Similarity NPC6095
0.6226 Remote Similarity NPC261831
0.6226 Remote Similarity NPC85813

  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 NPC31551 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
0.8684 High Similarity NPD3206 Approved
0.8462 Intermediate Similarity NPD9448 Phase 2
0.8462 Intermediate Similarity NPD633 Phase 3
0.8462 Intermediate Similarity NPD9655 Approved
0.8333 Intermediate Similarity NPD2699 Approved
0.8049 Intermediate Similarity NPD2270 Approved
0.7857 Intermediate Similarity NPD387 Clinical (unspecified phase)
0.7778 Intermediate Similarity NPD6125 Clinical (unspecified phase)
0.75 Intermediate Similarity NPD3199 Clinical (unspecified phase)
0.7333 Intermediate Similarity NPD634 Phase 3
0.72 Intermediate Similarity NPD3728 Approved
0.72 Intermediate Similarity NPD3730 Approved
0.7073 Intermediate Similarity NPD9449 Clinical (unspecified phase)
0.6863 Remote Similarity NPD3729 Clinical (unspecified phase)
0.6667 Remote Similarity NPD2266 Phase 2
0.6667 Remote Similarity NPD622 Approved
0.66 Remote Similarity NPD29 Approved
0.66 Remote Similarity NPD28 Approved
0.6596 Remote Similarity NPD9430 Approved
0.6596 Remote Similarity NPD9431 Approved
0.6585 Remote Similarity NPD9447 Approved
0.6471 Remote Similarity NPD3186 Phase 1
0.6364 Remote Similarity NPD9450 Approved
0.6364 Remote Similarity NPD77 Approved
0.6346 Remote Similarity NPD3172 Approved
0.6341 Remote Similarity NPD900 Approved
0.6275 Remote Similarity NPD9638 Phase 2
0.625 Remote Similarity NPD1461 Approved
0.625 Remote Similarity NPD908 Approved
0.625 Remote Similarity NPD907 Approved
0.6226 Remote Similarity NPD3196 Approved
0.6226 Remote Similarity NPD3194 Approved
0.6226 Remote Similarity NPD615 Clinical (unspecified phase)
0.6226 Remote Similarity NPD3195 Phase 2
0.6226 Remote Similarity NPD4266 Approved
0.6136 Remote Similarity NPD9513 Phase 1
0.5965 Remote Similarity NPD3198 Approved
0.5918 Remote Similarity NPD3174 Discontinued
0.5833 Remote Similarity NPD7909 Approved
0.575 Remote Similarity NPD62 Approved
0.5714 Remote Similarity NPD8278 Approved
0.5682 Remote Similarity NPD370 Phase 3
0.5625 Remote Similarity NPD8277 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