Structure

Physi-Chem Properties

Molecular Weight:  170.13
Volume:  193.824
LogP:  2.375
LogD:  2.365
LogS:  -2.997
# Rotatable Bonds:  6
TPSA:  26.3
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.36
Synthetic Accessibility Score:  2.454
Fsp3:  0.7
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -4.499
MDCK Permeability:  3.246411506552249e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.92
30% Bioavailability (F30%):  0.985

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.993
Plasma Protein Binding (PPB):  55.36355972290039%
Volume Distribution (VD):  1.171
Pgp-substrate:  48.408119201660156%

ADMET: Metabolism

CYP1A2-inhibitor:  0.845
CYP1A2-substrate:  0.746
CYP2C19-inhibitor:  0.409
CYP2C19-substrate:  0.885
CYP2C9-inhibitor:  0.114
CYP2C9-substrate:  0.713
CYP2D6-inhibitor:  0.04
CYP2D6-substrate:  0.695
CYP3A4-inhibitor:  0.056
CYP3A4-substrate:  0.292

ADMET: Excretion

Clearance (CL):  7.478
Half-life (T1/2):  0.911

ADMET: Toxicity

hERG Blockers:  0.05
Human Hepatotoxicity (H-HT):  0.034
Drug-inuced Liver Injury (DILI):  0.031
AMES Toxicity:  0.052
Rat Oral Acute Toxicity:  0.032
Maximum Recommended Daily Dose:  0.018
Skin Sensitization:  0.645
Carcinogencity:  0.69
Eye Corrosion:  0.892
Eye Irritation:  0.953
Respiratory Toxicity:  0.198

Download Data

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

  Natural Product: NPC187922

Natural Product ID:  NPC187922
Common Name*:   [(Z)-Hex-3-Enyl] 2-Methylpropanoate
IUPAC Name:   [(Z)-hex-3-enyl] 2-methylpropanoate
Synonyms:  
Standard InCHIKey:  OSMAJVWUIUORGC-WAYWQWQTSA-N
Standard InCHI:  InChI=1S/C10H18O2/c1-4-5-6-7-8-12-10(11)9(2)3/h5-6,9H,4,7-8H2,1-3H3/b6-5-
SMILES:  CC/C=CCCOC(=O)C(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3183445
PubChem CID:   5352539
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0001093] Carboxylic acid derivatives
          • [CHEMONTID:0001238] Carboxylic 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
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. cone n.a. PMID[10336650]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[15679315]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[16252923]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. cone n.a. PMID[17624889]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[18611049]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[18768384]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[19476340]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[21912858]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. cone n.a. PMID[22111577]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. flower n.a. PMID[22166201]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[23790907]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[24948953]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[25564559]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. PMID[29154541]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO18681 Artemisia scoparia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO18681 Artemisia scoparia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO18681 Artemisia scoparia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO13879 Humulus lupulus Species Cannabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO18681 Artemisia scoparia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13879 Humulus lupulus Species Cannabaceae 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. 21875.1 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 54947.7 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 NPC187922 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
0.9487 High Similarity NPC123357
0.8974 High Similarity NPC226511
0.8085 Intermediate Similarity NPC15789
0.7872 Intermediate Similarity NPC163345
0.7727 Intermediate Similarity NPC57923
0.7609 Intermediate Similarity NPC26600
0.7609 Intermediate Similarity NPC47946
0.7551 Intermediate Similarity NPC244452
0.75 Intermediate Similarity NPC477778
0.75 Intermediate Similarity NPC135698
0.7447 Intermediate Similarity NPC197467
0.74 Intermediate Similarity NPC170167
0.7347 Intermediate Similarity NPC289388
0.7347 Intermediate Similarity NPC236338
0.72 Intermediate Similarity NPC148056
0.7143 Intermediate Similarity NPC207815
0.7059 Intermediate Similarity NPC151919
0.7045 Intermediate Similarity NPC200147
0.7 Intermediate Similarity NPC27264
0.6923 Remote Similarity NPC127696
0.6875 Remote Similarity NPC270706
0.6852 Remote Similarity NPC252860
0.6852 Remote Similarity NPC327388
0.6809 Remote Similarity NPC270796
0.68 Remote Similarity NPC15912
0.6792 Remote Similarity NPC478120
0.6792 Remote Similarity NPC137538
0.6735 Remote Similarity NPC128280
0.6731 Remote Similarity NPC106531
0.6731 Remote Similarity NPC216407
0.6727 Remote Similarity NPC323597
0.6727 Remote Similarity NPC323498
0.6727 Remote Similarity NPC211752
0.6667 Remote Similarity NPC478117
0.6667 Remote Similarity NPC28779
0.6667 Remote Similarity NPC52264
0.6667 Remote Similarity NPC12907
0.6667 Remote Similarity NPC223677
0.6667 Remote Similarity NPC10316
0.6667 Remote Similarity NPC63354
0.6667 Remote Similarity NPC200845
0.6667 Remote Similarity NPC128061
0.6667 Remote Similarity NPC275316
0.6607 Remote Similarity NPC254095
0.6607 Remote Similarity NPC478096
0.6604 Remote Similarity NPC477780
0.6604 Remote Similarity NPC477781
0.6604 Remote Similarity NPC71761
0.6545 Remote Similarity NPC96663
0.6545 Remote Similarity NPC221763
0.6538 Remote Similarity NPC48162
0.6531 Remote Similarity NPC117572
0.6491 Remote Similarity NPC286189
0.6491 Remote Similarity NPC82465
0.6491 Remote Similarity NPC478095
0.6481 Remote Similarity NPC159535
0.6481 Remote Similarity NPC151761
0.6481 Remote Similarity NPC269615
0.6471 Remote Similarity NPC234597
0.6458 Remote Similarity NPC106819
0.6441 Remote Similarity NPC179087
0.6441 Remote Similarity NPC210303
0.6441 Remote Similarity NPC44343
0.6441 Remote Similarity NPC474658
0.6429 Remote Similarity NPC135863
0.6429 Remote Similarity NPC129150
0.6429 Remote Similarity NPC294938
0.6429 Remote Similarity NPC168714
0.6429 Remote Similarity NPC178643
0.6429 Remote Similarity NPC35371
0.6429 Remote Similarity NPC41007
0.6429 Remote Similarity NPC249850
0.6429 Remote Similarity NPC293437
0.64 Remote Similarity NPC42304
0.6379 Remote Similarity NPC130953
0.6364 Remote Similarity NPC474913
0.6333 Remote Similarity NPC34883
0.6327 Remote Similarity NPC6963
0.6327 Remote Similarity NPC304079
0.6316 Remote Similarity NPC21946
0.6316 Remote Similarity NPC223679
0.6296 Remote Similarity NPC309606
0.6296 Remote Similarity NPC139545
0.6296 Remote Similarity NPC39633
0.6275 Remote Similarity NPC91495
0.6271 Remote Similarity NPC151648
0.6271 Remote Similarity NPC320305
0.6271 Remote Similarity NPC328776
0.625 Remote Similarity NPC150717
0.625 Remote Similarity NPC245002
0.623 Remote Similarity NPC182794
0.623 Remote Similarity NPC133904
0.623 Remote Similarity NPC273600
0.6226 Remote Similarity NPC43053
0.6226 Remote Similarity NPC178586
0.6222 Remote Similarity NPC185839
0.6222 Remote Similarity NPC254764
0.6222 Remote Similarity NPC195109
0.6207 Remote Similarity NPC22897
0.6207 Remote Similarity NPC159650
0.62 Remote Similarity NPC172042
0.617 Remote Similarity NPC101147
0.617 Remote Similarity NPC12319
0.617 Remote Similarity NPC8270
0.617 Remote Similarity NPC18205
0.617 Remote Similarity NPC281043
0.6167 Remote Similarity NPC473737
0.6154 Remote Similarity NPC149821
0.6154 Remote Similarity NPC201132
0.6154 Remote Similarity NPC91765
0.6154 Remote Similarity NPC5413
0.6154 Remote Similarity NPC211250
0.614 Remote Similarity NPC265551
0.614 Remote Similarity NPC323436
0.614 Remote Similarity NPC472445
0.614 Remote Similarity NPC471279
0.614 Remote Similarity NPC165808
0.614 Remote Similarity NPC471277
0.614 Remote Similarity NPC44542
0.614 Remote Similarity NPC212730
0.6136 Remote Similarity NPC155872
0.6136 Remote Similarity NPC72258
0.6129 Remote Similarity NPC475555
0.6129 Remote Similarity NPC475675
0.6111 Remote Similarity NPC191643
0.6102 Remote Similarity NPC477424
0.6102 Remote Similarity NPC309408
0.6102 Remote Similarity NPC81896
0.6102 Remote Similarity NPC19241
0.6102 Remote Similarity NPC98519
0.6102 Remote Similarity NPC26223
0.6102 Remote Similarity NPC321919
0.6102 Remote Similarity NPC79756
0.6102 Remote Similarity NPC229252
0.6102 Remote Similarity NPC143857
0.6094 Remote Similarity NPC199557
0.6087 Remote Similarity NPC92863
0.6087 Remote Similarity NPC155880
0.6087 Remote Similarity NPC180840
0.6078 Remote Similarity NPC474204
0.6078 Remote Similarity NPC477776
0.6078 Remote Similarity NPC22098
0.6078 Remote Similarity NPC87137
0.6078 Remote Similarity NPC276009
0.6078 Remote Similarity NPC308331
0.6078 Remote Similarity NPC195246
0.6071 Remote Similarity NPC46151
0.6071 Remote Similarity NPC477984
0.6071 Remote Similarity NPC173157
0.6071 Remote Similarity NPC474672
0.6071 Remote Similarity NPC228473
0.6066 Remote Similarity NPC68343
0.6066 Remote Similarity NPC328089
0.6066 Remote Similarity NPC469723
0.6047 Remote Similarity NPC63121
0.6047 Remote Similarity NPC197356
0.6042 Remote Similarity NPC33489
0.6042 Remote Similarity NPC221250
0.6042 Remote Similarity NPC159773
0.6038 Remote Similarity NPC301482
0.6038 Remote Similarity NPC142103
0.6038 Remote Similarity NPC224227
0.6038 Remote Similarity NPC221467
0.6038 Remote Similarity NPC59051
0.6034 Remote Similarity NPC469373
0.6034 Remote Similarity NPC189700
0.6032 Remote Similarity NPC225272
0.6032 Remote Similarity NPC194871
0.6 Remote Similarity NPC59558
0.6 Remote Similarity NPC38497
0.6 Remote Similarity NPC312547
0.6 Remote Similarity NPC201939
0.6 Remote Similarity NPC75204
0.6 Remote Similarity NPC65353
0.6 Remote Similarity NPC113293
0.6 Remote Similarity NPC55376
0.5968 Remote Similarity NPC471566
0.5968 Remote Similarity NPC478098
0.5968 Remote Similarity NPC478099
0.5965 Remote Similarity NPC230296
0.5965 Remote Similarity NPC141699
0.5962 Remote Similarity NPC207292
0.5962 Remote Similarity NPC216130
0.5957 Remote Similarity NPC33761
0.5957 Remote Similarity NPC171978
0.5957 Remote Similarity NPC277382
0.5952 Remote Similarity NPC21374
0.5938 Remote Similarity NPC474823
0.5938 Remote Similarity NPC470256
0.5938 Remote Similarity NPC209327
0.5938 Remote Similarity NPC273508
0.5932 Remote Similarity NPC133600
0.5932 Remote Similarity NPC302564
0.5932 Remote Similarity NPC322186
0.5932 Remote Similarity NPC222852
0.5932 Remote Similarity NPC474267
0.5932 Remote Similarity NPC329249
0.5926 Remote Similarity NPC477777
0.5926 Remote Similarity NPC28205
0.5926 Remote Similarity NPC284212

  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 NPC187922 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
0.8182 Intermediate Similarity NPD6097 Approved
0.8182 Intermediate Similarity NPD6096 Approved
0.766 Intermediate Similarity NPD5343 Approved
0.72 Intermediate Similarity NPD6927 Phase 3
0.6809 Remote Similarity NPD5326 Phase 3
0.6531 Remote Similarity NPD3174 Discontinued
0.6531 Remote Similarity NPD4222 Approved
0.6531 Remote Similarity NPD39 Approved
0.6316 Remote Similarity NPD6109 Phase 1
0.6154 Remote Similarity NPD3173 Approved
0.6154 Remote Similarity NPD4220 Pre-registration
0.5957 Remote Similarity NPD5783 Phase 3
0.5926 Remote Similarity NPD28 Approved
0.5926 Remote Similarity NPD29 Approved
0.5806 Remote Similarity NPD5325 Clinical (unspecified phase)
0.5714 Remote Similarity NPD3172 Approved
0.5614 Remote Similarity NPD3194 Approved
0.5614 Remote Similarity NPD3196 Approved
0.5614 Remote Similarity NPD3195 Phase 2
0.5614 Remote Similarity NPD4266 Approved
0.56 Remote Similarity NPD9091 Suspended
0.56 Remote Similarity NPD9297 Discontinued

  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