Structure

Physi-Chem Properties

Molecular Weight:  88.05
Volume:  92.684
LogP:  0.697
LogD:  0.573
LogS:  -0.263
# Rotatable Bonds:  2
TPSA:  26.3
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  0
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.438
Synthetic Accessibility Score:  1.945
Fsp3:  0.75
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:  -4.178
MDCK Permeability:  4.1939885704778135e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.02
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.603

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.995
Plasma Protein Binding (PPB):  15.190900802612305%
Volume Distribution (VD):  0.788
Pgp-substrate:  82.509033203125%

ADMET: Metabolism

CYP1A2-inhibitor:  0.491
CYP1A2-substrate:  0.517
CYP2C19-inhibitor:  0.114
CYP2C19-substrate:  0.831
CYP2C9-inhibitor:  0.011
CYP2C9-substrate:  0.362
CYP2D6-inhibitor:  0.009
CYP2D6-substrate:  0.412
CYP3A4-inhibitor:  0.01
CYP3A4-substrate:  0.295

ADMET: Excretion

Clearance (CL):  9.275
Half-life (T1/2):  0.854

ADMET: Toxicity

hERG Blockers:  0.015
Human Hepatotoxicity (H-HT):  0.092
Drug-inuced Liver Injury (DILI):  0.218
AMES Toxicity:  0.01
Rat Oral Acute Toxicity:  0.024
Maximum Recommended Daily Dose:  0.045
Skin Sensitization:  0.445
Carcinogencity:  0.077
Eye Corrosion:  0.966
Eye Irritation:  0.98
Respiratory Toxicity:  0.088

Download Data

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

  Natural Product: NPC8187

Natural Product ID:  NPC8187
Common Name*:   Methyl Propanoate
IUPAC Name:   methyl propanoate
Synonyms:  
Standard InCHIKey:  RJUFJBKOKNCXHH-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C4H8O2/c1-3-4(5)6-2/h3H2,1-2H3
SMILES:  CCC(=O)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3183973
PubChem CID:   11124
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
            • [CHEMONTID:0003416] Methyl 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
NPT2 Others Unspecified Potency n.a. 196.9 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 49463.9 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 4905.2 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 NPC8187 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
0.913 High Similarity NPC32280
0.913 High Similarity NPC28246
0.913 High Similarity NPC41485
0.9091 High Similarity NPC203105
0.875 High Similarity NPC166804
0.8696 High Similarity NPC110107
0.84 Intermediate Similarity NPC143211
0.8333 Intermediate Similarity NPC3693
0.8261 Intermediate Similarity NPC23508
0.8095 Intermediate Similarity NPC137050
0.8077 Intermediate Similarity NPC55956
0.8 Intermediate Similarity NPC201132
0.8 Intermediate Similarity NPC211250
0.8 Intermediate Similarity NPC127134
0.7778 Intermediate Similarity NPC180423
0.7778 Intermediate Similarity NPC127696
0.7727 Intermediate Similarity NPC37493
0.7692 Intermediate Similarity NPC248233
0.75 Intermediate Similarity NPC265882
0.75 Intermediate Similarity NPC5934
0.75 Intermediate Similarity NPC208021
0.75 Intermediate Similarity NPC302611
0.75 Intermediate Similarity NPC21374
0.7407 Intermediate Similarity NPC317739
0.7407 Intermediate Similarity NPC88135
0.7407 Intermediate Similarity NPC281943
0.7391 Intermediate Similarity NPC260610
0.7308 Intermediate Similarity NPC314668
0.7308 Intermediate Similarity NPC149209
0.7308 Intermediate Similarity NPC230726
0.7241 Intermediate Similarity NPC12904
0.72 Intermediate Similarity NPC8368
0.7083 Intermediate Similarity NPC181153
0.7 Intermediate Similarity NPC41007
0.7 Intermediate Similarity NPC322892
0.7 Intermediate Similarity NPC286695
0.7 Intermediate Similarity NPC35371
0.7 Intermediate Similarity NPC108238
0.7 Intermediate Similarity NPC178643
0.7 Intermediate Similarity NPC168714
0.6923 Remote Similarity NPC35155
0.68 Remote Similarity NPC2419
0.6786 Remote Similarity NPC234005
0.6774 Remote Similarity NPC154396
0.6774 Remote Similarity NPC57499
0.6667 Remote Similarity NPC40965
0.6667 Remote Similarity NPC281883
0.6562 Remote Similarity NPC325165
0.6562 Remote Similarity NPC155872
0.6552 Remote Similarity NPC104195
0.6552 Remote Similarity NPC174368
0.6552 Remote Similarity NPC312003
0.6552 Remote Similarity NPC61066
0.6552 Remote Similarity NPC122768
0.6552 Remote Similarity NPC151140
0.6552 Remote Similarity NPC232172
0.6522 Remote Similarity NPC283245
0.6522 Remote Similarity NPC171188
0.6522 Remote Similarity NPC68873
0.6522 Remote Similarity NPC211453
0.6452 Remote Similarity NPC217218
0.6452 Remote Similarity NPC99700
0.6429 Remote Similarity NPC283626
0.64 Remote Similarity NPC37479
0.64 Remote Similarity NPC222945
0.6364 Remote Similarity NPC80641
0.6364 Remote Similarity NPC80396
0.6364 Remote Similarity NPC321699
0.6364 Remote Similarity NPC24967
0.6364 Remote Similarity NPC154642
0.6364 Remote Similarity NPC103612
0.6333 Remote Similarity NPC198126
0.625 Remote Similarity NPC173862
0.625 Remote Similarity NPC147212
0.625 Remote Similarity NPC63354
0.625 Remote Similarity NPC140229
0.625 Remote Similarity NPC286498
0.6207 Remote Similarity NPC231957
0.6207 Remote Similarity NPC159398
0.6176 Remote Similarity NPC14608
0.6176 Remote Similarity NPC206924
0.6154 Remote Similarity NPC185768
0.6154 Remote Similarity NPC33928
0.6154 Remote Similarity NPC133819
0.6129 Remote Similarity NPC328569
0.6129 Remote Similarity NPC212144
0.6129 Remote Similarity NPC280532
0.6071 Remote Similarity NPC286233
0.6061 Remote Similarity NPC301398
0.6061 Remote Similarity NPC289344
0.6061 Remote Similarity NPC223374
0.6061 Remote Similarity NPC196442
0.6061 Remote Similarity NPC191084
0.6061 Remote Similarity NPC168052
0.6061 Remote Similarity NPC250870
0.6061 Remote Similarity NPC86545
0.6061 Remote Similarity NPC316685
0.6 Remote Similarity NPC54980
0.6 Remote Similarity NPC248139
0.6 Remote Similarity NPC201622
0.6 Remote Similarity NPC292641
0.6 Remote Similarity NPC22903
0.6 Remote Similarity NPC305660
0.6 Remote Similarity NPC141986
0.5938 Remote Similarity NPC14778
0.5938 Remote Similarity NPC175342
0.5926 Remote Similarity NPC164646
0.5926 Remote Similarity NPC30338
0.5882 Remote Similarity NPC65353
0.5882 Remote Similarity NPC5505
0.5833 Remote Similarity NPC31551
0.5833 Remote Similarity NPC328688
0.5833 Remote Similarity NPC1502
0.5833 Remote Similarity NPC81263
0.5833 Remote Similarity NPC94368
0.5833 Remote Similarity NPC80234
0.5833 Remote Similarity NPC219536
0.5806 Remote Similarity NPC320981
0.5806 Remote Similarity NPC16947
0.5806 Remote Similarity NPC241404
0.5769 Remote Similarity NPC32603
0.5769 Remote Similarity NPC83723
0.5769 Remote Similarity NPC308490
0.5758 Remote Similarity NPC7814
0.5758 Remote Similarity NPC307027
0.5758 Remote Similarity NPC127142
0.5714 Remote Similarity NPC304927
0.5714 Remote Similarity NPC128996
0.5714 Remote Similarity NPC289974
0.5676 Remote Similarity NPC250028
0.5676 Remote Similarity NPC161097
0.5676 Remote Similarity NPC40597
0.5676 Remote Similarity NPC28598
0.5676 Remote Similarity NPC256163
0.5676 Remote Similarity NPC149299
0.5676 Remote Similarity NPC123357
0.5667 Remote Similarity NPC236709
0.5667 Remote Similarity NPC316272
0.5625 Remote Similarity NPC307739
0.5625 Remote Similarity NPC76217
0.5625 Remote Similarity NPC228727
0.56 Remote Similarity NPC237869
0.56 Remote Similarity NPC43196

  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 NPC8187 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
0.8095 Intermediate Similarity NPD8200 Phase 2
0.8 Intermediate Similarity NPD8989 Approved
0.7826 Intermediate Similarity NPD8615 Phase 2
0.7826 Intermediate Similarity NPD8616 Clinical (unspecified phase)
0.75 Intermediate Similarity NPD8856 Phase 2
0.7083 Intermediate Similarity NPD8201 Phase 2
0.7037 Intermediate Similarity NPD8990 Clinical (unspecified phase)
0.6923 Remote Similarity NPD8188 Approved
0.6774 Remote Similarity NPD900 Approved
0.6667 Remote Similarity NPD49 Approved
0.6667 Remote Similarity NPD7365 Approved
0.6667 Remote Similarity NPD105 Approved
0.6667 Remote Similarity NPD47 Approved
0.6667 Remote Similarity NPD7362 Approved
0.6667 Remote Similarity NPD50 Approved
0.6667 Remote Similarity NPD7363 Approved
0.6667 Remote Similarity NPD9636 Phase 2
0.6667 Remote Similarity NPD48 Approved
0.6562 Remote Similarity NPD9136 Clinical (unspecified phase)
0.6552 Remote Similarity NPD9191 Approved
0.6522 Remote Similarity NPD7364 Approved
0.6429 Remote Similarity NPD106 Approved
0.64 Remote Similarity NPD8190 Phase 2
0.6333 Remote Similarity NPD8618 Approved
0.6296 Remote Similarity NPD8592 Approved
0.6296 Remote Similarity NPD8591 Approved
0.6176 Remote Similarity NPD9131 Discovery
0.6071 Remote Similarity NPD8189 Approved
0.6 Remote Similarity NPD8619 Approved
0.6 Remote Similarity NPD8617 Approved
0.6 Remote Similarity NPD62 Approved
0.5806 Remote Similarity NPD54 Approved
0.5806 Remote Similarity NPD8206 Approved
0.5806 Remote Similarity NPD8590 Approved
0.5806 Remote Similarity NPD8204 Approved
0.5806 Remote Similarity NPD55 Approved
0.5806 Remote Similarity NPD8203 Approved
0.5806 Remote Similarity NPD9114 Clinical (unspecified phase)
0.5769 Remote Similarity NPD8191 Clinical (unspecified phase)
0.5758 Remote Similarity NPD8857 Approved
0.5714 Remote Similarity NPD9115 Approved
0.5667 Remote Similarity NPD8594 Approved
0.5667 Remote Similarity NPD8593 Approved
0.5652 Remote Similarity NPD8547 Phase 2
0.5625 Remote Similarity NPD8202 Approved
0.5625 Remote Similarity NPD8205 Approved
0.56 Remote Similarity NPD7356 Approved
0.56 Remote Similarity NPD7357 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