Structure

Physi-Chem Properties

Molecular Weight:  198.16
Volume:  228.416
LogP:  3.406
LogD:  3.568
LogS:  -3.767
# Rotatable Bonds:  9
TPSA:  26.3
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.339
Synthetic Accessibility Score:  2.188
Fsp3:  0.75
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:  -4.546
MDCK Permeability:  4.549261211650446e-05
Pgp-inhibitor:  0.045
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.929
30% Bioavailability (F30%):  0.992

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.977
Plasma Protein Binding (PPB):  90.32559967041016%
Volume Distribution (VD):  0.625
Pgp-substrate:  11.940709114074707%

ADMET: Metabolism

CYP1A2-inhibitor:  0.974
CYP1A2-substrate:  0.752
CYP2C19-inhibitor:  0.765
CYP2C19-substrate:  0.483
CYP2C9-inhibitor:  0.562
CYP2C9-substrate:  0.858
CYP2D6-inhibitor:  0.164
CYP2D6-substrate:  0.598
CYP3A4-inhibitor:  0.347
CYP3A4-substrate:  0.193

ADMET: Excretion

Clearance (CL):  8.989
Half-life (T1/2):  0.907

ADMET: Toxicity

hERG Blockers:  0.122
Human Hepatotoxicity (H-HT):  0.049
Drug-inuced Liver Injury (DILI):  0.027
AMES Toxicity:  0.054
Rat Oral Acute Toxicity:  0.061
Maximum Recommended Daily Dose:  0.031
Skin Sensitization:  0.913
Carcinogencity:  0.561
Eye Corrosion:  0.937
Eye Irritation:  0.958
Respiratory Toxicity:  0.262

Download Data

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

  Natural Product: NPC163345

Natural Product ID:  NPC163345
Common Name*:   [(Z)-Hex-3-Enyl] Hexanoate
IUPAC Name:   [(Z)-hex-3-enyl] hexanoate
Synonyms:  
Standard InCHIKey:  RGACQXBDYBCJCY-ALCCZGGFSA-N
Standard InCHI:  InChI=1S/C12H22O2/c1-3-5-7-9-11-14-12(13)10-8-6-4-2/h5,7H,3-4,6,8-11H2,1-2H3/b7-5-
SMILES:  CCCCCC(=O)OCC/C=CCC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3187552
PubChem CID:   5352543
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
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]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. fruit n.a. PMID[25172746]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[8910532]
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]
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]
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]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota Tissue Culture n.a. n.a. Database[FooDB]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7255 Pterocarpus indicus Species Fabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7255 Pterocarpus indicus Species Fabaceae 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]
NPO16501 Capsicum annuum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7255 Pterocarpus indicus Species Fabaceae 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. 2187.5 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 NPC163345 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
0.8462 Intermediate Similarity NPC200845
0.8462 Intermediate Similarity NPC28779
0.8462 Intermediate Similarity NPC223677
0.8462 Intermediate Similarity NPC10316
0.8462 Intermediate Similarity NPC128061
0.8431 Intermediate Similarity NPC71761
0.8222 Intermediate Similarity NPC123357
0.8125 Intermediate Similarity NPC172042
0.8077 Intermediate Similarity NPC139545
0.8077 Intermediate Similarity NPC39633
0.8077 Intermediate Similarity NPC309606
0.8 Intermediate Similarity NPC149821
0.8 Intermediate Similarity NPC207815
0.8 Intermediate Similarity NPC5413
0.7963 Intermediate Similarity NPC327388
0.7925 Intermediate Similarity NPC137538
0.7885 Intermediate Similarity NPC170167
0.7885 Intermediate Similarity NPC216407
0.7872 Intermediate Similarity NPC187922
0.7843 Intermediate Similarity NPC224227
0.7818 Intermediate Similarity NPC211752
0.7818 Intermediate Similarity NPC323498
0.7818 Intermediate Similarity NPC323597
0.78 Intermediate Similarity NPC216130
0.78 Intermediate Similarity NPC207292
0.7778 Intermediate Similarity NPC52264
0.7778 Intermediate Similarity NPC228473
0.7778 Intermediate Similarity NPC226511
0.7719 Intermediate Similarity NPC229252
0.7719 Intermediate Similarity NPC143857
0.7692 Intermediate Similarity NPC244452
0.7692 Intermediate Similarity NPC284212
0.7692 Intermediate Similarity NPC28205
0.7692 Intermediate Similarity NPC262968
0.7647 Intermediate Similarity NPC250919
0.7627 Intermediate Similarity NPC328089
0.7627 Intermediate Similarity NPC68343
0.7586 Intermediate Similarity NPC320305
0.7586 Intermediate Similarity NPC328776
0.7586 Intermediate Similarity NPC201939
0.7547 Intermediate Similarity NPC92114
0.7547 Intermediate Similarity NPC281245
0.7544 Intermediate Similarity NPC478095
0.75 Intermediate Similarity NPC289388
0.7458 Intermediate Similarity NPC54925
0.7451 Intermediate Similarity NPC91495
0.7414 Intermediate Similarity NPC243532
0.7407 Intermediate Similarity NPC36061
0.7407 Intermediate Similarity NPC321062
0.7407 Intermediate Similarity NPC70387
0.7407 Intermediate Similarity NPC294548
0.7407 Intermediate Similarity NPC139029
0.7407 Intermediate Similarity NPC1813
0.74 Intermediate Similarity NPC117572
0.7368 Intermediate Similarity NPC478096
0.7333 Intermediate Similarity NPC80396
0.7333 Intermediate Similarity NPC154642
0.7308 Intermediate Similarity NPC135698
0.7288 Intermediate Similarity NPC113293
0.7273 Intermediate Similarity NPC87564
0.7273 Intermediate Similarity NPC281972
0.7273 Intermediate Similarity NPC154245
0.7273 Intermediate Similarity NPC290563
0.7273 Intermediate Similarity NPC32467
0.7273 Intermediate Similarity NPC85813
0.7273 Intermediate Similarity NPC88966
0.7273 Intermediate Similarity NPC25417
0.7273 Intermediate Similarity NPC424
0.7273 Intermediate Similarity NPC261831
0.7273 Intermediate Similarity NPC6095
0.7255 Intermediate Similarity NPC42304
0.7222 Intermediate Similarity NPC161366
0.7222 Intermediate Similarity NPC310746
0.7193 Intermediate Similarity NPC323436
0.717 Intermediate Similarity NPC59051
0.7143 Intermediate Similarity NPC473863
0.7143 Intermediate Similarity NPC274290
0.7143 Intermediate Similarity NPC474672
0.7119 Intermediate Similarity NPC321919
0.7119 Intermediate Similarity NPC81896
0.7037 Intermediate Similarity NPC48162
0.7031 Intermediate Similarity NPC199557
0.7031 Intermediate Similarity NPC317583
0.7018 Intermediate Similarity NPC187777
0.7018 Intermediate Similarity NPC477201
0.7018 Intermediate Similarity NPC18951
0.7018 Intermediate Similarity NPC252860
0.7018 Intermediate Similarity NPC179764
0.7 Intermediate Similarity NPC321838
0.6984 Remote Similarity NPC22101
0.6984 Remote Similarity NPC475443
0.6984 Remote Similarity NPC330426
0.6984 Remote Similarity NPC271921
0.6984 Remote Similarity NPC148192
0.6984 Remote Similarity NPC25298
0.6984 Remote Similarity NPC104537
0.6984 Remote Similarity NPC473829
0.6984 Remote Similarity NPC127091
0.6949 Remote Similarity NPC329249
0.6949 Remote Similarity NPC22897
0.6949 Remote Similarity NPC159650
0.6897 Remote Similarity NPC225929
0.6889 Remote Similarity NPC154396
0.6885 Remote Similarity NPC474774
0.6875 Remote Similarity NPC324981
0.6875 Remote Similarity NPC48218
0.6875 Remote Similarity NPC81263
0.6875 Remote Similarity NPC218477
0.6875 Remote Similarity NPC80234
0.6875 Remote Similarity NPC141481
0.6875 Remote Similarity NPC473559
0.6852 Remote Similarity NPC15789
0.6842 Remote Similarity NPC54766
0.6833 Remote Similarity NPC327112
0.6833 Remote Similarity NPC45097
0.6833 Remote Similarity NPC328311
0.6825 Remote Similarity NPC248125
0.68 Remote Similarity NPC57923
0.6792 Remote Similarity NPC180534
0.678 Remote Similarity NPC469373
0.6774 Remote Similarity NPC34883
0.6774 Remote Similarity NPC226592
0.6774 Remote Similarity NPC470320
0.6769 Remote Similarity NPC130618
0.6769 Remote Similarity NPC473772
0.6735 Remote Similarity NPC250028
0.6735 Remote Similarity NPC256163
0.6735 Remote Similarity NPC149299
0.6735 Remote Similarity NPC40597
0.6731 Remote Similarity NPC26600
0.6731 Remote Similarity NPC47946
0.6731 Remote Similarity NPC239754
0.6727 Remote Similarity NPC470411
0.6724 Remote Similarity NPC325977
0.6721 Remote Similarity NPC151648
0.6719 Remote Similarity NPC49863
0.6719 Remote Similarity NPC26500
0.6719 Remote Similarity NPC478097
0.6719 Remote Similarity NPC478100
0.6719 Remote Similarity NPC99619
0.6667 Remote Similarity NPC155880
0.6667 Remote Similarity NPC136164
0.6667 Remote Similarity NPC322461
0.6667 Remote Similarity NPC476654
0.6667 Remote Similarity NPC329550
0.6667 Remote Similarity NPC476655
0.6667 Remote Similarity NPC472955
0.6667 Remote Similarity NPC286695
0.6667 Remote Similarity NPC234597
0.6667 Remote Similarity NPC274927
0.6667 Remote Similarity NPC478098
0.6667 Remote Similarity NPC318420
0.6667 Remote Similarity NPC255863
0.6667 Remote Similarity NPC474267
0.6667 Remote Similarity NPC92863
0.6667 Remote Similarity NPC106851
0.6667 Remote Similarity NPC323045
0.6667 Remote Similarity NPC42526
0.6667 Remote Similarity NPC477778
0.6667 Remote Similarity NPC320642
0.6667 Remote Similarity NPC317881
0.6667 Remote Similarity NPC245947
0.6667 Remote Similarity NPC270796
0.6667 Remote Similarity NPC322892
0.6667 Remote Similarity NPC133904
0.6667 Remote Similarity NPC476657
0.6667 Remote Similarity NPC326268
0.6667 Remote Similarity NPC475310
0.6667 Remote Similarity NPC323477
0.6667 Remote Similarity NPC476660
0.6667 Remote Similarity NPC478099
0.6618 Remote Similarity NPC92558
0.6613 Remote Similarity NPC474658
0.6607 Remote Similarity NPC106531
0.6607 Remote Similarity NPC151919
0.6607 Remote Similarity NPC129458
0.6604 Remote Similarity NPC44363
0.6604 Remote Similarity NPC110234
0.6604 Remote Similarity NPC163751
0.6604 Remote Similarity NPC197467
0.66 Remote Similarity NPC53541
0.6596 Remote Similarity NPC80641
0.6567 Remote Similarity NPC163003
0.6567 Remote Similarity NPC320119
0.6562 Remote Similarity NPC154728
0.6562 Remote Similarity NPC476656
0.6562 Remote Similarity NPC126899
0.6562 Remote Similarity NPC304665
0.6562 Remote Similarity NPC328653
0.6562 Remote Similarity NPC476659
0.6562 Remote Similarity NPC478101
0.6557 Remote Similarity NPC299730
0.6557 Remote Similarity NPC122521
0.6557 Remote Similarity NPC235242
0.6557 Remote Similarity NPC26223
0.6557 Remote Similarity NPC251042
0.6557 Remote Similarity NPC174447
0.6552 Remote Similarity NPC477984
0.6552 Remote Similarity NPC46151
0.6545 Remote Similarity NPC27264

  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 NPC163345 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
0.8542 High Similarity NPD5343 Approved
0.8511 High Similarity NPD3174 Discontinued
0.8 Intermediate Similarity NPD3173 Approved
0.7917 Intermediate Similarity NPD6097 Approved
0.7917 Intermediate Similarity NPD6096 Approved
0.7692 Intermediate Similarity NPD28 Approved
0.7692 Intermediate Similarity NPD29 Approved
0.7407 Intermediate Similarity NPD3172 Approved
0.74 Intermediate Similarity NPD4222 Approved
0.7273 Intermediate Similarity NPD4266 Approved
0.7273 Intermediate Similarity NPD3194 Approved
0.7273 Intermediate Similarity NPD3195 Phase 2
0.7273 Intermediate Similarity NPD3196 Approved
0.7059 Intermediate Similarity NPD39 Approved
0.7037 Intermediate Similarity NPD6927 Phase 3
0.6833 Remote Similarity NPD4246 Clinical (unspecified phase)
0.6792 Remote Similarity NPD622 Approved
0.678 Remote Similarity NPD6109 Phase 1
0.6774 Remote Similarity NPD3197 Phase 1
0.6719 Remote Similarity NPD4247 Clinical (unspecified phase)
0.6667 Remote Similarity NPD5326 Phase 3
0.6286 Remote Similarity NPD8039 Approved
0.6226 Remote Similarity NPD2699 Approved
0.6061 Remote Similarity NPD6108 Clinical (unspecified phase)
0.5909 Remote Similarity NPD2685 Clinical (unspecified phase)
0.5893 Remote Similarity NPD2266 Phase 2
0.5893 Remote Similarity NPD6125 Clinical (unspecified phase)
0.5867 Remote Similarity NPD5790 Clinical (unspecified phase)
0.5844 Remote Similarity NPD7154 Phase 3
0.5789 Remote Similarity NPD5369 Approved
0.5714 Remote Similarity NPD6435 Approved
0.5686 Remote Similarity NPD3206 Approved
0.5676 Remote Similarity NPD4756 Discovery
0.5658 Remote Similarity NPD4252 Approved
0.5641 Remote Similarity NPD5362 Discontinued
0.56 Remote Similarity NPD5784 Clinical (unspecified phase)
0.56 Remote Similarity NPD4271 Approved
0.56 Remote Similarity NPD4268 Approved
0.56 Remote Similarity NPD3732 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