Structure

Physi-Chem Properties

Molecular Weight:  258.18
Volume:  280.588
LogP:  3.772
LogD:  4.223
LogS:  -3.925
# Rotatable Bonds:  11
TPSA:  52.6
# H-Bond Aceptor:  4
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.471
Synthetic Accessibility Score:  2.018
Fsp3:  0.857
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.421
MDCK Permeability:  3.0632516427431256e-05
Pgp-inhibitor:  0.976
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.05
30% Bioavailability (F30%):  0.891

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.52
Plasma Protein Binding (PPB):  82.18418884277344%
Volume Distribution (VD):  0.569
Pgp-substrate:  14.844051361083984%

ADMET: Metabolism

CYP1A2-inhibitor:  0.45
CYP1A2-substrate:  0.092
CYP2C19-inhibitor:  0.364
CYP2C19-substrate:  0.395
CYP2C9-inhibitor:  0.753
CYP2C9-substrate:  0.753
CYP2D6-inhibitor:  0.008
CYP2D6-substrate:  0.036
CYP3A4-inhibitor:  0.088
CYP3A4-substrate:  0.256

ADMET: Excretion

Clearance (CL):  13.002
Half-life (T1/2):  0.915

ADMET: Toxicity

hERG Blockers:  0.021
Human Hepatotoxicity (H-HT):  0.048
Drug-inuced Liver Injury (DILI):  0.356
AMES Toxicity:  0.011
Rat Oral Acute Toxicity:  0.045
Maximum Recommended Daily Dose:  0.013
Skin Sensitization:  0.932
Carcinogencity:  0.159
Eye Corrosion:  0.964
Eye Irritation:  0.911
Respiratory Toxicity:  0.043

Download Data

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

  Natural Product: NPC81263

Natural Product ID:  NPC81263
Common Name*:   Bis(2-Methylpropyl) Hexanedioate
IUPAC Name:   bis(2-methylpropyl) hexanedioate
Synonyms:  
Standard InCHIKey:  RDOFJDLLWVCMRU-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C14H26O4/c1-11(2)9-17-13(15)7-5-6-8-14(16)18-10-12(3)4/h11-12H,5-10H2,1-4H3
SMILES:  CC(COC(=O)CCCCC(=O)OCC(C)C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3184260
PubChem CID:   8831
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
NPO6947 Astilbe chinensis Species Saxifragaceae Eukaryota rhizomes n.a. n.a. PMID[19585998]
NPO6947 Astilbe chinensis Species Saxifragaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6947 Astilbe chinensis Species Saxifragaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6947 Astilbe chinensis Species Saxifragaceae 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
NPT2 Others Unspecified Potency n.a. 21872.4 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 76958.8 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 NPC81263 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
0.9167 High Similarity NPC154642
0.9167 High Similarity NPC80396
0.8919 High Similarity NPC14608
0.8889 High Similarity NPC155872
0.8611 High Similarity NPC154396
0.8611 High Similarity NPC57499
0.8571 High Similarity NPC308301
0.85 High Similarity NPC53541
0.8462 Intermediate Similarity NPC80234
0.8372 Intermediate Similarity NPC249754
0.8333 Intermediate Similarity NPC322892
0.8333 Intermediate Similarity NPC286695
0.825 Intermediate Similarity NPC250028
0.825 Intermediate Similarity NPC149299
0.825 Intermediate Similarity NPC256163
0.825 Intermediate Similarity NPC40597
0.8158 Intermediate Similarity NPC80641
0.8056 Intermediate Similarity NPC40965
0.8056 Intermediate Similarity NPC12904
0.8 Intermediate Similarity NPC223249
0.8 Intermediate Similarity NPC219536
0.8 Intermediate Similarity NPC31551
0.7895 Intermediate Similarity NPC289344
0.7857 Intermediate Similarity NPC236579
0.7857 Intermediate Similarity NPC203531
0.7838 Intermediate Similarity NPC35371
0.7838 Intermediate Similarity NPC168714
0.7838 Intermediate Similarity NPC178643
0.7838 Intermediate Similarity NPC41007
0.7805 Intermediate Similarity NPC165533
0.775 Intermediate Similarity NPC201622
0.775 Intermediate Similarity NPC305660
0.775 Intermediate Similarity NPC22903
0.775 Intermediate Similarity NPC54980
0.775 Intermediate Similarity NPC316546
0.7727 Intermediate Similarity NPC282440
0.7632 Intermediate Similarity NPC286498
0.7561 Intermediate Similarity NPC94368
0.75 Intermediate Similarity NPC127696
0.75 Intermediate Similarity NPC287231
0.75 Intermediate Similarity NPC47363
0.7447 Intermediate Similarity NPC305182
0.7436 Intermediate Similarity NPC196442
0.7436 Intermediate Similarity NPC223374
0.7436 Intermediate Similarity NPC301398
0.7436 Intermediate Similarity NPC86545
0.7381 Intermediate Similarity NPC161097
0.7381 Intermediate Similarity NPC12156
0.7381 Intermediate Similarity NPC28598
0.7333 Intermediate Similarity NPC145045
0.7333 Intermediate Similarity NPC172042
0.7333 Intermediate Similarity NPC52700
0.7333 Intermediate Similarity NPC105329
0.7333 Intermediate Similarity NPC63182
0.7297 Intermediate Similarity NPC21374
0.7292 Intermediate Similarity NPC314084
0.7273 Intermediate Similarity NPC317128
0.7209 Intermediate Similarity NPC248763
0.7209 Intermediate Similarity NPC325452
0.7174 Intermediate Similarity NPC326957
0.7111 Intermediate Similarity NPC273545
0.7083 Intermediate Similarity NPC55678
0.7073 Intermediate Similarity NPC252843
0.7073 Intermediate Similarity NPC128996
0.7045 Intermediate Similarity NPC176500
0.7045 Intermediate Similarity NPC325102
0.7 Intermediate Similarity NPC317203
0.7 Intermediate Similarity NPC156630
0.6957 Remote Similarity NPC30195
0.6957 Remote Similarity NPC12438
0.6944 Remote Similarity NPC143211
0.6944 Remote Similarity NPC248233
0.6939 Remote Similarity NPC287811
0.6923 Remote Similarity NPC328710
0.6923 Remote Similarity NPC108238
0.6923 Remote Similarity NPC99700
0.6923 Remote Similarity NPC175342
0.6923 Remote Similarity NPC18224
0.6905 Remote Similarity NPC73245
0.6875 Remote Similarity NPC26253
0.6875 Remote Similarity NPC250919
0.6875 Remote Similarity NPC163345
0.6829 Remote Similarity NPC321699
0.6757 Remote Similarity NPC317739
0.6757 Remote Similarity NPC281943
0.6744 Remote Similarity NPC294085
0.6744 Remote Similarity NPC113928
0.6744 Remote Similarity NPC301696
0.6744 Remote Similarity NPC214610
0.6744 Remote Similarity NPC201844
0.6744 Remote Similarity NPC279026
0.6744 Remote Similarity NPC154186
0.6744 Remote Similarity NPC3531
0.6744 Remote Similarity NPC261080
0.6744 Remote Similarity NPC118968
0.6744 Remote Similarity NPC301585
0.6744 Remote Similarity NPC183424
0.6744 Remote Similarity NPC14227
0.6739 Remote Similarity NPC55023
0.6739 Remote Similarity NPC312547
0.6667 Remote Similarity NPC211250
0.6667 Remote Similarity NPC106872
0.6667 Remote Similarity NPC201132
0.6667 Remote Similarity NPC166804
0.6596 Remote Similarity NPC314679
0.6545 Remote Similarity NPC470363
0.6538 Remote Similarity NPC53463
0.6538 Remote Similarity NPC23155
0.6538 Remote Similarity NPC320588
0.6538 Remote Similarity NPC469937
0.6512 Remote Similarity NPC268826
0.65 Remote Similarity NPC147054
0.6471 Remote Similarity NPC170167
0.6471 Remote Similarity NPC310746
0.6471 Remote Similarity NPC216407
0.6458 Remote Similarity NPC328497
0.6458 Remote Similarity NPC324004
0.6458 Remote Similarity NPC21844
0.6444 Remote Similarity NPC163746
0.6444 Remote Similarity NPC103286
0.6444 Remote Similarity NPC149184
0.6444 Remote Similarity NPC209970
0.6444 Remote Similarity NPC307783
0.6444 Remote Similarity NPC196924
0.6444 Remote Similarity NPC216630
0.6444 Remote Similarity NPC171736
0.6429 Remote Similarity NPC134782
0.6429 Remote Similarity NPC155263
0.6389 Remote Similarity NPC3693
0.6389 Remote Similarity NPC28246
0.6389 Remote Similarity NPC32280
0.6389 Remote Similarity NPC41485
0.6341 Remote Similarity NPC140229
0.6327 Remote Similarity NPC324793
0.6327 Remote Similarity NPC68577
0.6327 Remote Similarity NPC477878
0.6327 Remote Similarity NPC200618
0.6327 Remote Similarity NPC13105
0.6327 Remote Similarity NPC131770
0.6327 Remote Similarity NPC216130
0.6316 Remote Similarity NPC159398
0.6304 Remote Similarity NPC301528
0.6304 Remote Similarity NPC67462
0.6304 Remote Similarity NPC129972
0.6304 Remote Similarity NPC71317
0.6279 Remote Similarity NPC206924
0.6279 Remote Similarity NPC109026
0.6279 Remote Similarity NPC158179
0.6275 Remote Similarity NPC244452
0.625 Remote Similarity NPC226602
0.625 Remote Similarity NPC472020
0.625 Remote Similarity NPC472019
0.6226 Remote Similarity NPC319589
0.62 Remote Similarity NPC223675
0.62 Remote Similarity NPC304162
0.619 Remote Similarity NPC218357
0.617 Remote Similarity NPC19305
0.617 Remote Similarity NPC255837
0.617 Remote Similarity NPC74845
0.6154 Remote Similarity NPC180423
0.6154 Remote Similarity NPC174368
0.614 Remote Similarity NPC472021
0.614 Remote Similarity NPC45097
0.6136 Remote Similarity NPC325454
0.6111 Remote Similarity NPC223677
0.6111 Remote Similarity NPC128061
0.6111 Remote Similarity NPC200845
0.6111 Remote Similarity NPC28779
0.6111 Remote Similarity NPC10316
0.6111 Remote Similarity NPC110107
0.6102 Remote Similarity NPC314103
0.6078 Remote Similarity NPC90904
0.6078 Remote Similarity NPC142103
0.6078 Remote Similarity NPC289388
0.6042 Remote Similarity NPC8219
0.6038 Remote Similarity NPC71761
0.6038 Remote Similarity NPC72722
0.6034 Remote Similarity NPC306750
0.6 Remote Similarity NPC473936
0.6 Remote Similarity NPC265882
0.5965 Remote Similarity NPC475821
0.5965 Remote Similarity NPC17935
0.5965 Remote Similarity NPC125506
0.5962 Remote Similarity NPC470411
0.5962 Remote Similarity NPC100096
0.5962 Remote Similarity NPC291724
0.5962 Remote Similarity NPC274261
0.5957 Remote Similarity NPC289686
0.5918 Remote Similarity NPC133771
0.5909 Remote Similarity NPC69245
0.5902 Remote Similarity NPC135043
0.5902 Remote Similarity NPC315525
0.5897 Remote Similarity NPC234005
0.5854 Remote Similarity NPC281883
0.5854 Remote Similarity NPC49151
0.5854 Remote Similarity NPC262505
0.5854 Remote Similarity NPC179831
0.5854 Remote Similarity NPC254713
0.5854 Remote Similarity NPC261991
0.5854 Remote Similarity NPC280532

  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 NPC81263 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
0.7778 Intermediate Similarity NPD2266 Phase 2
0.75 Intermediate Similarity NPD9449 Clinical (unspecified phase)
0.75 Intermediate Similarity NPD2699 Approved
0.7391 Intermediate Similarity NPD6125 Clinical (unspecified phase)
0.7179 Intermediate Similarity NPD900 Approved
0.7 Intermediate Similarity NPD9447 Approved
0.6905 Remote Similarity NPD3206 Approved
0.6744 Remote Similarity NPD9655 Approved
0.6744 Remote Similarity NPD633 Phase 3
0.6744 Remote Similarity NPD9450 Approved
0.6744 Remote Similarity NPD9448 Phase 2
0.6744 Remote Similarity NPD77 Approved
0.6667 Remote Similarity NPD387 Clinical (unspecified phase)
0.6596 Remote Similarity NPD634 Phase 3
0.6538 Remote Similarity NPD3728 Approved
0.6538 Remote Similarity NPD3730 Approved
0.6444 Remote Similarity NPD2270 Approved
0.6226 Remote Similarity NPD3729 Clinical (unspecified phase)
0.6222 Remote Similarity NPD9635 Discontinued
0.6182 Remote Similarity NPD4279 Approved
0.6047 Remote Similarity NPD370 Phase 3
0.6042 Remote Similarity NPD3199 Clinical (unspecified phase)
0.6038 Remote Similarity NPD631 Approved
0.6038 Remote Similarity NPD630 Approved
0.6 Remote Similarity NPD5343 Approved
0.5965 Remote Similarity NPD4280 Approved
0.5918 Remote Similarity NPD3174 Discontinued
0.5854 Remote Similarity NPD9636 Phase 2
0.5849 Remote Similarity NPD3186 Phase 1
0.5789 Remote Similarity NPD8989 Approved
0.575 Remote Similarity NPD62 Approved
0.5714 Remote Similarity NPD377 Approved
0.569 Remote Similarity NPD3198 Approved
0.566 Remote Similarity NPD9638 Phase 2
0.566 Remote Similarity NPD1400 Approved
0.566 Remote Similarity NPD1399 Approved
0.5641 Remote Similarity NPD8990 Clinical (unspecified phase)
0.5636 Remote Similarity NPD615 Clinical (unspecified phase)
0.561 Remote Similarity NPD8856 Phase 2

  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