Structure

Physi-Chem Properties

Molecular Weight:  170.13
Volume:  187.904
LogP:  3.167
LogD:  2.622
LogS:  -2.917
# Rotatable Bonds:  4
TPSA:  26.3
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.479
Synthetic Accessibility Score:  2.645
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:  -4.48
MDCK Permeability:  4.0192328015109524e-05
Pgp-inhibitor:  0.963
Pgp-substrate:  0.004
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.021
30% Bioavailability (F30%):  0.943

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.919
Plasma Protein Binding (PPB):  88.92516326904297%
Volume Distribution (VD):  0.651
Pgp-substrate:  13.758148193359375%

ADMET: Metabolism

CYP1A2-inhibitor:  0.286
CYP1A2-substrate:  0.297
CYP2C19-inhibitor:  0.094
CYP2C19-substrate:  0.26
CYP2C9-inhibitor:  0.049
CYP2C9-substrate:  0.867
CYP2D6-inhibitor:  0.078
CYP2D6-substrate:  0.36
CYP3A4-inhibitor:  0.211
CYP3A4-substrate:  0.207

ADMET: Excretion

Clearance (CL):  8.655
Half-life (T1/2):  0.684

ADMET: Toxicity

hERG Blockers:  0.018
Human Hepatotoxicity (H-HT):  0.127
Drug-inuced Liver Injury (DILI):  0.133
AMES Toxicity:  0.016
Rat Oral Acute Toxicity:  0.014
Maximum Recommended Daily Dose:  0.745
Skin Sensitization:  0.937
Carcinogencity:  0.61
Eye Corrosion:  0.951
Eye Irritation:  0.903
Respiratory Toxicity:  0.187

Download Data

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

  Natural Product: NPC326957

Natural Product ID:  NPC326957
Common Name*:   6-Pentyloxan-2-One
IUPAC Name:   6-pentyloxan-2-one
Synonyms:  
Standard InCHIKey:  GHBSPIPJMLAMEP-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C10H18O2/c1-2-3-4-6-9-7-5-8-10(11)12-9/h9H,2-8H2,1H3
SMILES:  CCCCCC1CCCC(=O)O1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3182189
PubChem CID:   12810
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000050] Lactones
        • [CHEMONTID:0001244] Delta valerolactones

*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
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. Nigeria(latitude 80°N and longitude 4°E) 2005; 2006 DOI[10.1002/ejlt.201000080]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s11306-010-0259-y]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s11306-014-0638-x]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. DOI[10.1007/s11746-997-0093-1]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. DOI[10.1016/j.phytol.2008.07.007]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Seeds Plovdiv, Plovdiv region in South Bulgaria DOI[10.1051/CTV/20163101031]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. PMID[11170689]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. leaf n.a. PMID[11312782]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. fruit n.a. PMID[11312782]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. PMID[11408943]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. fruit n.a. PMID[12105962]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. Esuela Tecnica Superior de Ingenieros Agrónomos de Albacete 2007 PMID[19256538]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. PMID[20826702]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. PMID[22537213]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. PMID[23759170]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Stalks n.a. n.a. PMID[24521157]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Seeds Benedictine Pannonhalma Archabbey, Hungary PMID[29803478]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. PMID[31433178]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Stem n.a. n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Fruits n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Leaf n.a. n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota Leaf Essent. Oil n.a. n.a. Database[FooDB]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17024 Vitis vinifera Species Vitaceae 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. 61659.9 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 68589.6 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 NPC326957 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
0.8667 High Similarity NPC47363
0.8667 High Similarity NPC287231
0.8605 High Similarity NPC256163
0.8605 High Similarity NPC40597
0.8605 High Similarity NPC149299
0.8605 High Similarity NPC250028
0.8478 Intermediate Similarity NPC105329
0.8478 Intermediate Similarity NPC145045
0.8478 Intermediate Similarity NPC63182
0.8478 Intermediate Similarity NPC52700
0.8409 Intermediate Similarity NPC53541
0.8372 Intermediate Similarity NPC223249
0.8372 Intermediate Similarity NPC80234
0.8261 Intermediate Similarity NPC273545
0.8222 Intermediate Similarity NPC203531
0.8222 Intermediate Similarity NPC236579
0.8182 Intermediate Similarity NPC165533
0.814 Intermediate Similarity NPC201622
0.814 Intermediate Similarity NPC54980
0.814 Intermediate Similarity NPC305660
0.814 Intermediate Similarity NPC22903
0.7955 Intermediate Similarity NPC31551
0.7955 Intermediate Similarity NPC219536
0.7826 Intermediate Similarity NPC176500
0.78 Intermediate Similarity NPC55678
0.7778 Intermediate Similarity NPC12156
0.7778 Intermediate Similarity NPC161097
0.7778 Intermediate Similarity NPC28598
0.7755 Intermediate Similarity NPC106872
0.7674 Intermediate Similarity NPC80396
0.7674 Intermediate Similarity NPC80641
0.7674 Intermediate Similarity NPC154642
0.766 Intermediate Similarity NPC317128
0.7647 Intermediate Similarity NPC287811
0.7647 Intermediate Similarity NPC314084
0.7551 Intermediate Similarity NPC328497
0.7551 Intermediate Similarity NPC324004
0.7442 Intermediate Similarity NPC223374
0.7442 Intermediate Similarity NPC156630
0.7442 Intermediate Similarity NPC196442
0.7442 Intermediate Similarity NPC86545
0.7442 Intermediate Similarity NPC301398
0.74 Intermediate Similarity NPC131770
0.74 Intermediate Similarity NPC200618
0.7347 Intermediate Similarity NPC12438
0.7347 Intermediate Similarity NPC30195
0.7255 Intermediate Similarity NPC304162
0.7255 Intermediate Similarity NPC26253
0.7222 Intermediate Similarity NPC53463
0.7222 Intermediate Similarity NPC469937
0.7222 Intermediate Similarity NPC23155
0.7222 Intermediate Similarity NPC320588
0.7209 Intermediate Similarity NPC154396
0.7209 Intermediate Similarity NPC286498
0.7174 Intermediate Similarity NPC301696
0.7174 Intermediate Similarity NPC301585
0.7174 Intermediate Similarity NPC261080
0.7174 Intermediate Similarity NPC113928
0.7174 Intermediate Similarity NPC201844
0.7174 Intermediate Similarity NPC14227
0.7174 Intermediate Similarity NPC279026
0.7174 Intermediate Similarity NPC94368
0.7174 Intermediate Similarity NPC154186
0.7174 Intermediate Similarity NPC81263
0.7119 Intermediate Similarity NPC235788
0.7115 Intermediate Similarity NPC90904
0.7115 Intermediate Similarity NPC305182
0.7111 Intermediate Similarity NPC128996
0.6977 Remote Similarity NPC322892
0.6977 Remote Similarity NPC99700
0.6977 Remote Similarity NPC286695
0.6939 Remote Similarity NPC74845
0.6923 Remote Similarity NPC250919
0.6897 Remote Similarity NPC472019
0.6897 Remote Similarity NPC226602
0.6897 Remote Similarity NPC472020
0.6897 Remote Similarity NPC469924
0.6875 Remote Similarity NPC149184
0.6875 Remote Similarity NPC307783
0.6875 Remote Similarity NPC196924
0.6875 Remote Similarity NPC216630
0.6875 Remote Similarity NPC209970
0.6875 Remote Similarity NPC171736
0.6863 Remote Similarity NPC249754
0.6852 Remote Similarity NPC310746
0.6818 Remote Similarity NPC57499
0.6809 Remote Similarity NPC294085
0.6809 Remote Similarity NPC118968
0.6809 Remote Similarity NPC183424
0.6809 Remote Similarity NPC214610
0.68 Remote Similarity NPC469781
0.678 Remote Similarity NPC472021
0.6744 Remote Similarity NPC40965
0.6744 Remote Similarity NPC12904
0.6739 Remote Similarity NPC14608
0.6735 Remote Similarity NPC67462
0.6731 Remote Similarity NPC216130
0.6667 Remote Similarity NPC308301
0.6667 Remote Similarity NPC282440
0.6667 Remote Similarity NPC289344
0.6667 Remote Similarity NPC155872
0.6667 Remote Similarity NPC100096
0.6613 Remote Similarity NPC157518
0.6613 Remote Similarity NPC469926
0.661 Remote Similarity NPC475821
0.661 Remote Similarity NPC470363
0.661 Remote Similarity NPC17935
0.6607 Remote Similarity NPC319589
0.66 Remote Similarity NPC255837
0.66 Remote Similarity NPC19305
0.66 Remote Similarity NPC76051
0.6596 Remote Similarity NPC268826
0.6557 Remote Similarity NPC325773
0.6522 Remote Similarity NPC155263
0.6522 Remote Similarity NPC321699
0.6515 Remote Similarity NPC320119
0.6491 Remote Similarity NPC223677
0.6491 Remote Similarity NPC10316
0.6491 Remote Similarity NPC28779
0.6491 Remote Similarity NPC200845
0.6491 Remote Similarity NPC128061
0.6471 Remote Similarity NPC55023
0.6471 Remote Similarity NPC8219
0.6462 Remote Similarity NPC475062
0.6462 Remote Similarity NPC98711
0.6429 Remote Similarity NPC71761
0.6415 Remote Similarity NPC13105
0.6406 Remote Similarity NPC206601
0.6364 Remote Similarity NPC274261
0.6364 Remote Similarity NPC291724
0.6349 Remote Similarity NPC306805
0.6349 Remote Similarity NPC215987
0.6346 Remote Similarity NPC314679
0.6346 Remote Similarity NPC172042
0.6324 Remote Similarity NPC477867
0.629 Remote Similarity NPC54925
0.629 Remote Similarity NPC474552
0.6269 Remote Similarity NPC96322
0.625 Remote Similarity NPC316546
0.625 Remote Similarity NPC161366
0.6232 Remote Similarity NPC471491
0.623 Remote Similarity NPC229252
0.623 Remote Similarity NPC143857
0.6226 Remote Similarity NPC21844
0.6222 Remote Similarity NPC147054
0.6212 Remote Similarity NPC317583
0.6212 Remote Similarity NPC285003
0.6212 Remote Similarity NPC241265
0.62 Remote Similarity NPC103286
0.62 Remote Similarity NPC163746
0.619 Remote Similarity NPC328089
0.619 Remote Similarity NPC68343
0.619 Remote Similarity NPC314103
0.617 Remote Similarity NPC301919
0.617 Remote Similarity NPC134782
0.6154 Remote Similarity NPC286842
0.614 Remote Similarity NPC39633
0.614 Remote Similarity NPC139545
0.614 Remote Similarity NPC309606
0.6136 Remote Similarity NPC168982
0.6129 Remote Similarity NPC201939
0.6129 Remote Similarity NPC469923
0.6129 Remote Similarity NPC469922
0.6129 Remote Similarity NPC253204
0.6129 Remote Similarity NPC306750
0.6111 Remote Similarity NPC68577
0.6111 Remote Similarity NPC324793
0.6111 Remote Similarity NPC477878
0.6094 Remote Similarity NPC326651
0.6094 Remote Similarity NPC325117
0.6094 Remote Similarity NPC322319
0.6078 Remote Similarity NPC289686
0.6078 Remote Similarity NPC129972
0.6078 Remote Similarity NPC301528
0.6078 Remote Similarity NPC71317
0.6061 Remote Similarity NPC97736
0.6061 Remote Similarity NPC50228
0.6061 Remote Similarity NPC82315
0.6056 Remote Similarity NPC83108
0.6056 Remote Similarity NPC214030
0.6056 Remote Similarity NPC474003
0.6038 Remote Similarity NPC133771
0.6029 Remote Similarity NPC184550
0.6029 Remote Similarity NPC478227
0.6029 Remote Similarity NPC185419
0.6029 Remote Similarity NPC470243
0.6 Remote Similarity NPC475861
0.6 Remote Similarity NPC163345
0.6 Remote Similarity NPC179831
0.6 Remote Similarity NPC49151
0.6 Remote Similarity NPC261991
0.6 Remote Similarity NPC220922
0.6 Remote Similarity NPC223675
0.6 Remote Similarity NPC315525
0.6 Remote Similarity NPC262505
0.6 Remote Similarity NPC135043
0.6 Remote Similarity NPC254713
0.597 Remote Similarity NPC199557
0.597 Remote Similarity NPC211428
0.597 Remote Similarity NPC178541

  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 NPC326957 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
0.8667 High Similarity NPD2699 Approved
0.7755 Intermediate Similarity NPD6125 Clinical (unspecified phase)
0.7333 Intermediate Similarity NPD3206 Approved
0.7222 Intermediate Similarity NPD3730 Approved
0.7222 Intermediate Similarity NPD3728 Approved
0.7174 Intermediate Similarity NPD633 Phase 3
0.7174 Intermediate Similarity NPD9448 Phase 2
0.6875 Remote Similarity NPD2270 Approved
0.6809 Remote Similarity NPD9655 Approved
0.6735 Remote Similarity NPD387 Clinical (unspecified phase)
0.6607 Remote Similarity NPD3729 Clinical (unspecified phase)
0.6471 Remote Similarity NPD3199 Clinical (unspecified phase)
0.6346 Remote Similarity NPD634 Phase 3
0.617 Remote Similarity NPD370 Phase 3
0.6111 Remote Similarity NPD2266 Phase 2
0.6066 Remote Similarity NPD3198 Approved
0.6042 Remote Similarity NPD9449 Clinical (unspecified phase)
0.6034 Remote Similarity NPD615 Clinical (unspecified phase)
0.6 Remote Similarity NPD8959 Approved
0.5938 Remote Similarity NPD7909 Approved
0.5833 Remote Similarity NPD73 Approved
0.5821 Remote Similarity NPD8278 Approved
0.5818 Remote Similarity NPD622 Approved
0.5797 Remote Similarity NPD5777 Approved
0.5789 Remote Similarity NPD1400 Approved
0.5789 Remote Similarity NPD29 Approved
0.5789 Remote Similarity NPD28 Approved
0.5789 Remote Similarity NPD1399 Approved
0.5775 Remote Similarity NPD3702 Approved
0.5745 Remote Similarity NPD900 Approved
0.5741 Remote Similarity NPD9430 Approved
0.5741 Remote Similarity NPD9431 Approved
0.5735 Remote Similarity NPD8277 Approved
0.5692 Remote Similarity NPD3197 Phase 1
0.569 Remote Similarity NPD3186 Phase 1
0.5672 Remote Similarity NPD896 Approved
0.5672 Remote Similarity NPD898 Approved
0.5672 Remote Similarity NPD897 Approved
0.5625 Remote Similarity NPD9447 Approved
0.5606 Remote Similarity NPD9496 Clinical (unspecified phase)

  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