Structure

Physi-Chem Properties

Molecular Weight:  172.15
Volume:  196.46
LogP:  3.79
LogD:  3.381
LogS:  -3.823
# Rotatable Bonds:  8
TPSA:  26.3
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.436
Synthetic Accessibility Score:  1.66
Fsp3:  0.9
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.387
MDCK Permeability:  2.848492658813484e-05
Pgp-inhibitor:  0.516
Pgp-substrate:  0.007
Human Intestinal Absorption (HIA):  0.002
20% Bioavailability (F20%):  0.879
30% Bioavailability (F30%):  0.964

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.875
Plasma Protein Binding (PPB):  89.46398162841797%
Volume Distribution (VD):  0.549
Pgp-substrate:  14.598470687866211%

ADMET: Metabolism

CYP1A2-inhibitor:  0.983
CYP1A2-substrate:  0.586
CYP2C19-inhibitor:  0.799
CYP2C19-substrate:  0.428
CYP2C9-inhibitor:  0.57
CYP2C9-substrate:  0.737
CYP2D6-inhibitor:  0.054
CYP2D6-substrate:  0.119
CYP3A4-inhibitor:  0.147
CYP3A4-substrate:  0.166

ADMET: Excretion

Clearance (CL):  11.326
Half-life (T1/2):  0.76

ADMET: Toxicity

hERG Blockers:  0.117
Human Hepatotoxicity (H-HT):  0.022
Drug-inuced Liver Injury (DILI):  0.088
AMES Toxicity:  0.006
Rat Oral Acute Toxicity:  0.068
Maximum Recommended Daily Dose:  0.015
Skin Sensitization:  0.87
Carcinogencity:  0.221
Eye Corrosion:  0.972
Eye Irritation:  0.983
Respiratory Toxicity:  0.31

Download Data

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

  Natural Product: NPC286695

Natural Product ID:  NPC286695
Common Name*:   Pentyl Pentanoate
IUPAC Name:   pentyl pentanoate
Synonyms:  
Standard InCHIKey:  FGPPDYNPZTUNIU-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C10H20O2/c1-3-5-7-9-12-10(11)8-6-4-2/h3-9H2,1-2H3
SMILES:  CCCCCOC(=O)CCCC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3187606
PubChem CID:   62433
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
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota Flowers n.a. n.a. DOI[10.1016/j.foodchem.2009.03.042]
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota Flowers n.a. n.a. DOI[10.3136/fstr.15.499]
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota Flowers n.a. n.a. DOI[10.5897/AJB10.140]
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota Flowers n.a. n.a. DOI[10.5897/AJB2010.000-3252]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. fruit n.a. PMID[12932131]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[20460582]
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota Flowers Tongxiang, China n.a. PMID[24621197]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. fruit n.a. PMID[25172746]
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota Flowers n.a. n.a. PMID[28248102]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[8910532]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Pericarp n.a. n.a. Database[FooDB]
NPO17752 Mentha X piperita Strain Lamiaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Resin, Exudate, Sap n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO17752 Mentha X piperita Strain Lamiaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Tissue Culture n.a. n.a. Database[FooDB]
NPO17752 Mentha X piperita Strain Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO17752 Mentha X piperita Strain Lamiaceae Eukaryota n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO17752 Mentha X piperita Strain Lamiaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17752 Mentha X piperita Strain Lamiaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17752 Mentha X piperita Strain Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO17752 Mentha X piperita Strain Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20440 Chrysanthemum x morifolium Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16501 Capsicum annuum Species Solanaceae 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
NPO17752 NPC286695 Other Leaf 0.055 0.01 0.1 mg/100g Database [DUKE]

☑ 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
NPT162 Individual Protein Heat shock protein beta-1 Homo sapiens Potency n.a. 54941 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 68589.6 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 30637.9 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 1949.4 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 NPC286695 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
0.9667 High Similarity NPC12904
0.9091 High Similarity NPC80396
0.9091 High Similarity NPC154642
0.9062 High Similarity NPC154396
0.875 High Similarity NPC322892
0.8529 High Similarity NPC80641
0.8438 Intermediate Similarity NPC40965
0.8333 Intermediate Similarity NPC81263
0.8333 Intermediate Similarity NPC80234
0.8333 Intermediate Similarity NPC248233
0.8333 Intermediate Similarity NPC143211
0.8286 Intermediate Similarity NPC14608
0.8235 Intermediate Similarity NPC155872
0.8182 Intermediate Similarity NPC178643
0.8182 Intermediate Similarity NPC35371
0.8182 Intermediate Similarity NPC99700
0.8182 Intermediate Similarity NPC168714
0.8182 Intermediate Similarity NPC41007
0.8108 Intermediate Similarity NPC40597
0.8108 Intermediate Similarity NPC256163
0.8108 Intermediate Similarity NPC250028
0.8108 Intermediate Similarity NPC149299
0.8 Intermediate Similarity NPC166804
0.8 Intermediate Similarity NPC321699
0.7941 Intermediate Similarity NPC286498
0.7941 Intermediate Similarity NPC57499
0.7895 Intermediate Similarity NPC53541
0.7838 Intermediate Similarity NPC223249
0.7812 Intermediate Similarity NPC127696
0.7714 Intermediate Similarity NPC86545
0.7714 Intermediate Similarity NPC223374
0.7714 Intermediate Similarity NPC301398
0.7714 Intermediate Similarity NPC289344
0.7714 Intermediate Similarity NPC196442
0.7692 Intermediate Similarity NPC236579
0.7692 Intermediate Similarity NPC203531
0.7667 Intermediate Similarity NPC41485
0.7667 Intermediate Similarity NPC28246
0.7667 Intermediate Similarity NPC3693
0.7667 Intermediate Similarity NPC32280
0.7647 Intermediate Similarity NPC108238
0.7632 Intermediate Similarity NPC165533
0.7576 Intermediate Similarity NPC21374
0.7568 Intermediate Similarity NPC305660
0.7568 Intermediate Similarity NPC201622
0.7568 Intermediate Similarity NPC54980
0.7568 Intermediate Similarity NPC22903
0.7368 Intermediate Similarity NPC219536
0.7368 Intermediate Similarity NPC94368
0.7368 Intermediate Similarity NPC31551
0.7333 Intermediate Similarity NPC110107
0.7317 Intermediate Similarity NPC47363
0.7317 Intermediate Similarity NPC287231
0.7297 Intermediate Similarity NPC128996
0.7273 Intermediate Similarity NPC174368
0.7179 Intermediate Similarity NPC28598
0.7179 Intermediate Similarity NPC161097
0.7179 Intermediate Similarity NPC12156
0.7143 Intermediate Similarity NPC308301
0.7143 Intermediate Similarity NPC172042
0.7143 Intermediate Similarity NPC145045
0.7143 Intermediate Similarity NPC52700
0.7143 Intermediate Similarity NPC105329
0.7143 Intermediate Similarity NPC63182
0.7105 Intermediate Similarity NPC316546
0.7 Intermediate Similarity NPC203105
0.7 Intermediate Similarity NPC23508
0.7 Intermediate Similarity NPC8187
0.6977 Remote Similarity NPC326957
0.6977 Remote Similarity NPC249754
0.697 Remote Similarity NPC234005
0.697 Remote Similarity NPC281943
0.697 Remote Similarity NPC317739
0.6944 Remote Similarity NPC140229
0.6905 Remote Similarity NPC273545
0.6875 Remote Similarity NPC201132
0.6875 Remote Similarity NPC211250
0.6875 Remote Similarity NPC127134
0.6842 Remote Similarity NPC206924
0.6842 Remote Similarity NPC158179
0.6829 Remote Similarity NPC176500
0.6829 Remote Similarity NPC325102
0.6765 Remote Similarity NPC180423
0.6765 Remote Similarity NPC248139
0.6757 Remote Similarity NPC317203
0.6757 Remote Similarity NPC156630
0.6744 Remote Similarity NPC12438
0.6744 Remote Similarity NPC30195
0.6744 Remote Similarity NPC282440
0.6667 Remote Similarity NPC317128
0.6667 Remote Similarity NPC175342
0.6667 Remote Similarity NPC147054
0.6667 Remote Similarity NPC163345
0.6667 Remote Similarity NPC217218
0.6667 Remote Similarity NPC73245
0.6667 Remote Similarity NPC26253
0.6667 Remote Similarity NPC250919
0.6571 Remote Similarity NPC302611
0.6571 Remote Similarity NPC5934
0.6571 Remote Similarity NPC265882
0.6522 Remote Similarity NPC305182
0.6522 Remote Similarity NPC55678
0.6512 Remote Similarity NPC312547
0.65 Remote Similarity NPC113928
0.65 Remote Similarity NPC201844
0.65 Remote Similarity NPC3531
0.65 Remote Similarity NPC261080
0.65 Remote Similarity NPC154186
0.65 Remote Similarity NPC301585
0.65 Remote Similarity NPC279026
0.65 Remote Similarity NPC301696
0.65 Remote Similarity NPC14227
0.6486 Remote Similarity NPC7814
0.6486 Remote Similarity NPC127142
0.6471 Remote Similarity NPC159398
0.6471 Remote Similarity NPC88135
0.6444 Remote Similarity NPC106872
0.6389 Remote Similarity NPC281883
0.6383 Remote Similarity NPC314084
0.6383 Remote Similarity NPC287811
0.6364 Remote Similarity NPC133771
0.6364 Remote Similarity NPC149209
0.6333 Remote Similarity NPC61373
0.625 Remote Similarity NPC310746
0.625 Remote Similarity NPC8368
0.625 Remote Similarity NPC164646
0.6222 Remote Similarity NPC324004
0.6222 Remote Similarity NPC328497
0.6216 Remote Similarity NPC125575
0.6216 Remote Similarity NPC328710
0.6216 Remote Similarity NPC18224
0.619 Remote Similarity NPC149184
0.619 Remote Similarity NPC171736
0.619 Remote Similarity NPC103286
0.619 Remote Similarity NPC307783
0.619 Remote Similarity NPC325452
0.619 Remote Similarity NPC196924
0.619 Remote Similarity NPC163746
0.619 Remote Similarity NPC248763
0.619 Remote Similarity NPC209970
0.619 Remote Similarity NPC216630
0.6176 Remote Similarity NPC283626
0.6154 Remote Similarity NPC155263
0.6111 Remote Similarity NPC198126
0.6098 Remote Similarity NPC474205
0.6098 Remote Similarity NPC118968
0.6098 Remote Similarity NPC294085
0.6098 Remote Similarity NPC225963
0.6098 Remote Similarity NPC183424
0.6098 Remote Similarity NPC214610
0.6087 Remote Similarity NPC216130
0.6087 Remote Similarity NPC68577
0.6087 Remote Similarity NPC131770
0.6087 Remote Similarity NPC200618
0.6047 Remote Similarity NPC71317
0.6047 Remote Similarity NPC129972
0.6047 Remote Similarity NPC301528
0.6047 Remote Similarity NPC67462
0.6 Remote Similarity NPC252843
0.6 Remote Similarity NPC55956
0.6 Remote Similarity NPC37493
0.6 Remote Similarity NPC109026
0.6 Remote Similarity NPC53463
0.6 Remote Similarity NPC23155
0.6 Remote Similarity NPC469937
0.6 Remote Similarity NPC320588
0.5957 Remote Similarity NPC135698
0.5957 Remote Similarity NPC223675
0.5957 Remote Similarity NPC304162
0.5952 Remote Similarity NPC123357
0.5946 Remote Similarity NPC179831
0.5946 Remote Similarity NPC254713
0.5946 Remote Similarity NPC280532
0.5946 Remote Similarity NPC261991
0.5946 Remote Similarity NPC262505
0.5946 Remote Similarity NPC49151
0.5938 Remote Similarity NPC208021
0.5918 Remote Similarity NPC170167
0.5909 Remote Similarity NPC74845
0.5909 Remote Similarity NPC319680
0.5909 Remote Similarity NPC255837
0.5909 Remote Similarity NPC19305
0.5897 Remote Similarity NPC316685
0.5897 Remote Similarity NPC191084
0.5897 Remote Similarity NPC250870
0.5897 Remote Similarity NPC168052
0.5882 Remote Similarity NPC10316
0.5882 Remote Similarity NPC28779
0.5882 Remote Similarity NPC223677
0.5882 Remote Similarity NPC128061
0.5882 Remote Similarity NPC200845
0.5882 Remote Similarity NPC59581
0.5854 Remote Similarity NPC268826
0.5854 Remote Similarity NPC325454
0.5854 Remote Similarity NPC38930
0.5833 Remote Similarity NPC122768
0.5833 Remote Similarity NPC232172
0.5833 Remote Similarity NPC312003
0.5833 Remote Similarity NPC104195
0.5833 Remote Similarity NPC90904

  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 NPC286695 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
0.7941 Intermediate Similarity NPD900 Approved
0.7317 Intermediate Similarity NPD2699 Approved
0.6875 Remote Similarity NPD8989 Approved
0.6818 Remote Similarity NPD5343 Approved
0.6818 Remote Similarity NPD2266 Phase 2
0.6818 Remote Similarity NPD6125 Clinical (unspecified phase)
0.6765 Remote Similarity NPD62 Approved
0.6757 Remote Similarity NPD9447 Approved
0.6667 Remote Similarity NPD8616 Clinical (unspecified phase)
0.6667 Remote Similarity NPD3206 Approved
0.6667 Remote Similarity NPD8615 Phase 2
0.6571 Remote Similarity NPD8856 Phase 2
0.65 Remote Similarity NPD633 Phase 3
0.65 Remote Similarity NPD9450 Approved
0.65 Remote Similarity NPD77 Approved
0.65 Remote Similarity NPD9448 Phase 2
0.6486 Remote Similarity NPD8857 Approved
0.641 Remote Similarity NPD9449 Clinical (unspecified phase)
0.6389 Remote Similarity NPD9636 Phase 2
0.619 Remote Similarity NPD2270 Approved
0.6176 Remote Similarity NPD8990 Clinical (unspecified phase)
0.6154 Remote Similarity NPD370 Phase 3
0.6136 Remote Similarity NPD6097 Approved
0.6136 Remote Similarity NPD377 Approved
0.6136 Remote Similarity NPD6096 Approved
0.6122 Remote Similarity NPD631 Approved
0.6122 Remote Similarity NPD630 Approved
0.6111 Remote Similarity NPD8618 Approved
0.6098 Remote Similarity NPD9655 Approved
0.6047 Remote Similarity NPD387 Clinical (unspecified phase)
0.6 Remote Similarity NPD3728 Approved
0.6 Remote Similarity NPD3730 Approved
0.5952 Remote Similarity NPD9635 Discontinued
0.587 Remote Similarity NPD1458 Approved
0.587 Remote Similarity NPD1459 Approved
0.5833 Remote Similarity NPD8619 Approved
0.5833 Remote Similarity NPD8617 Approved
0.5778 Remote Similarity NPD3199 Clinical (unspecified phase)
0.5714 Remote Similarity NPD106 Approved
0.5714 Remote Similarity NPD6927 Phase 3
0.5667 Remote Similarity NPD8200 Phase 2
0.5652 Remote Similarity NPD3174 Discontinued
0.5652 Remote Similarity NPD4222 Approved
0.5652 Remote Similarity NPD634 Phase 3
0.561 Remote Similarity NPD9131 Discovery

  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