Structure

Physi-Chem Properties

Molecular Weight:  130.1
Volume:  144.572
LogP:  2.155
LogD:  1.965
LogS:  -1.651
# Rotatable Bonds:  4
TPSA:  26.3
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.542
Synthetic Accessibility Score:  1.851
Fsp3:  0.857
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:  -4.151
MDCK Permeability:  3.2262178137898445e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.147
30% Bioavailability (F30%):  0.584

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.989
Plasma Protein Binding (PPB):  43.12063217163086%
Volume Distribution (VD):  1.003
Pgp-substrate:  66.2049331665039%

ADMET: Metabolism

CYP1A2-inhibitor:  0.912
CYP1A2-substrate:  0.114
CYP2C19-inhibitor:  0.205
CYP2C19-substrate:  0.75
CYP2C9-inhibitor:  0.185
CYP2C9-substrate:  0.446
CYP2D6-inhibitor:  0.011
CYP2D6-substrate:  0.139
CYP3A4-inhibitor:  0.02
CYP3A4-substrate:  0.261

ADMET: Excretion

Clearance (CL):  7.369
Half-life (T1/2):  0.739

ADMET: Toxicity

hERG Blockers:  0.014
Human Hepatotoxicity (H-HT):  0.026
Drug-inuced Liver Injury (DILI):  0.35
AMES Toxicity:  0.012
Rat Oral Acute Toxicity:  0.023
Maximum Recommended Daily Dose:  0.015
Skin Sensitization:  0.482
Carcinogencity:  0.31
Eye Corrosion:  0.971
Eye Irritation:  0.992
Respiratory Toxicity:  0.073

Download Data

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

  Natural Product: NPC281943

Natural Product ID:  NPC281943
Common Name*:   3-Methylbutyl Acetate
IUPAC Name:   3-methylbutyl acetate
Synonyms:   Acetic Acid 3-Methyl-Butyl Ester
Standard InCHIKey:  MLFHJEHSLIIPHL-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C7H14O2/c1-6(2)4-5-9-7(3)8/h6H,4-5H2,1-3H3
SMILES:  CC(CCOC(=O)C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL42013
PubChem CID:   31276
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

☑ 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
NPT150 Individual Protein Anthrax lethal factor Bacillus anthracis Potency = 12589.3 nM PMID[575703]
NPT10 Individual Protein Geminin Homo sapiens Potency n.a. 29092.9 nM PMID[575704]
NPT49 Individual Protein DNA-(apurinic or apyrimidinic site) lyase Homo sapiens Potency n.a. 1062.1 nM PMID[575704]
NPT27 Others Unspecified k cat = 34.0 s-1 PMID[575702]
NPT27 Others Unspecified Km = 3600000.0 nM PMID[575702]
NPT27 Others Unspecified Ratio = 93.0 n.a. PMID[575702]
NPT27 Others Unspecified Activity = 0.11 M-1 s-1 PMID[575702]
NPT2 Others Unspecified Potency n.a. 29092.9 nM PMID[575704]
NPT2 Others Unspecified Potency n.a. 691.9 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 NPC281943 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
1.0 High Similarity NPC317739
0.9286 High Similarity NPC21374
0.9231 High Similarity NPC201132
0.8846 High Similarity NPC3693
0.8667 High Similarity NPC178643
0.8667 High Similarity NPC35371
0.8667 High Similarity NPC168714
0.8667 High Similarity NPC41007
0.8519 High Similarity NPC166804
0.8462 Intermediate Similarity NPC110107
0.8276 Intermediate Similarity NPC127696
0.8214 Intermediate Similarity NPC143211
0.8214 Intermediate Similarity NPC248233
0.8148 Intermediate Similarity NPC32280
0.8148 Intermediate Similarity NPC41485
0.8077 Intermediate Similarity NPC23508
0.7857 Intermediate Similarity NPC127134
0.7857 Intermediate Similarity NPC211250
0.7647 Intermediate Similarity NPC14608
0.7576 Intermediate Similarity NPC155872
0.75 Intermediate Similarity NPC28246
0.7429 Intermediate Similarity NPC316546
0.7407 Intermediate Similarity NPC8187
0.7407 Intermediate Similarity NPC203105
0.7333 Intermediate Similarity NPC88135
0.7188 Intermediate Similarity NPC12904
0.7188 Intermediate Similarity NPC40965
0.7143 Intermediate Similarity NPC8368
0.7097 Intermediate Similarity NPC104195
0.7097 Intermediate Similarity NPC151140
0.7097 Intermediate Similarity NPC122768
0.7097 Intermediate Similarity NPC61066
0.7059 Intermediate Similarity NPC316685
0.697 Remote Similarity NPC286695
0.697 Remote Similarity NPC322892
0.697 Remote Similarity NPC108238
0.6923 Remote Similarity NPC37493
0.6875 Remote Similarity NPC265882
0.6875 Remote Similarity NPC5934
0.6786 Remote Similarity NPC208021
0.6774 Remote Similarity NPC234005
0.6765 Remote Similarity NPC140229
0.6765 Remote Similarity NPC154396
0.6765 Remote Similarity NPC286498
0.6757 Remote Similarity NPC81263
0.6667 Remote Similarity NPC325102
0.6667 Remote Similarity NPC230726
0.6667 Remote Similarity NPC280532
0.6667 Remote Similarity NPC281883
0.6571 Remote Similarity NPC223374
0.6571 Remote Similarity NPC196442
0.6571 Remote Similarity NPC301398
0.6571 Remote Similarity NPC86545
0.6562 Remote Similarity NPC312003
0.6562 Remote Similarity NPC180423
0.6562 Remote Similarity NPC232172
0.6538 Remote Similarity NPC137050
0.6471 Remote Similarity NPC99700
0.6471 Remote Similarity NPC217218
0.6389 Remote Similarity NPC154642
0.6389 Remote Similarity NPC65353
0.6389 Remote Similarity NPC80396
0.6389 Remote Similarity NPC321699
0.6389 Remote Similarity NPC80641
0.6364 Remote Similarity NPC302611
0.6333 Remote Similarity NPC289974
0.6333 Remote Similarity NPC304927
0.6333 Remote Similarity NPC35155
0.6316 Remote Similarity NPC316217
0.6316 Remote Similarity NPC222792
0.6286 Remote Similarity NPC63354
0.6286 Remote Similarity NPC307027
0.625 Remote Similarity NPC159398
0.625 Remote Similarity NPC231957
0.625 Remote Similarity NPC55956
0.6216 Remote Similarity NPC128996
0.6207 Remote Similarity NPC2419
0.6207 Remote Similarity NPC133819
0.619 Remote Similarity NPC282440
0.619 Remote Similarity NPC308301
0.6129 Remote Similarity NPC149209
0.6129 Remote Similarity NPC314668
0.6129 Remote Similarity NPC190117
0.6111 Remote Similarity NPC289344
0.6071 Remote Similarity NPC61373
0.6071 Remote Similarity NPC260610
0.6047 Remote Similarity NPC249754
0.6 Remote Similarity NPC256186
0.6 Remote Similarity NPC23071
0.5946 Remote Similarity NPC24967
0.5946 Remote Similarity NPC103612
0.5938 Remote Similarity NPC283626
0.5897 Remote Similarity NPC94368
0.5897 Remote Similarity NPC80234
0.5882 Remote Similarity NPC198126
0.5862 Remote Similarity NPC83723
0.5854 Remote Similarity NPC187922
0.5833 Remote Similarity NPC57499
0.5814 Remote Similarity NPC133771
0.5789 Remote Similarity NPC252843
0.5758 Remote Similarity NPC287782
0.575 Remote Similarity NPC250028
0.575 Remote Similarity NPC40597
0.575 Remote Similarity NPC256163
0.575 Remote Similarity NPC149299
0.5714 Remote Similarity NPC173862
0.5714 Remote Similarity NPC319680
0.5714 Remote Similarity NPC43196
0.5714 Remote Similarity NPC327092
0.5714 Remote Similarity NPC228727
0.5676 Remote Similarity NPC191084
0.5676 Remote Similarity NPC325165
0.5676 Remote Similarity NPC250870
0.5676 Remote Similarity NPC168052
0.5652 Remote Similarity NPC142103
0.5652 Remote Similarity NPC289388
0.5652 Remote Similarity NPC305182
0.5641 Remote Similarity NPC325454
0.5641 Remote Similarity NPC226511
0.5641 Remote Similarity NPC38930
0.5625 Remote Similarity NPC128335
0.561 Remote Similarity NPC159773
0.561 Remote Similarity NPC53541

  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 NPC281943 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
0.7857 Intermediate Similarity NPD8989 Approved
0.7 Intermediate Similarity NPD8990 Clinical (unspecified phase)
0.6875 Remote Similarity NPD8856 Phase 2
0.6765 Remote Similarity NPD900 Approved
0.6667 Remote Similarity NPD9636 Phase 2
0.6562 Remote Similarity NPD9191 Approved
0.6429 Remote Similarity NPD8616 Clinical (unspecified phase)
0.6429 Remote Similarity NPD8615 Phase 2
0.6129 Remote Similarity NPD57 Approved
0.6111 Remote Similarity NPD9447 Approved
0.5926 Remote Similarity NPD8200 Phase 2
0.5882 Remote Similarity NPD8618 Approved
0.5806 Remote Similarity NPD8188 Approved
0.5789 Remote Similarity NPD9449 Clinical (unspecified phase)
0.5789 Remote Similarity NPD9131 Discovery
0.5769 Remote Similarity NPD8547 Phase 2
0.5676 Remote Similarity NPD9136 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