Structure

Physi-Chem Properties

Molecular Weight:  104.05
Volume:  101.475
LogP:  -0.482
LogD:  -0.356
LogS:  0.709
# Rotatable Bonds:  2
TPSA:  46.53
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.458
Synthetic Accessibility Score:  2.729
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:  -4.54
MDCK Permeability:  0.0008919088868424296
Pgp-inhibitor:  0.0
Pgp-substrate:  0.021
Human Intestinal Absorption (HIA):  0.01
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.735

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.581
Plasma Protein Binding (PPB):  11.074321746826172%
Volume Distribution (VD):  0.804
Pgp-substrate:  86.14600372314453%

ADMET: Metabolism

CYP1A2-inhibitor:  0.088
CYP1A2-substrate:  0.478
CYP2C19-inhibitor:  0.036
CYP2C19-substrate:  0.702
CYP2C9-inhibitor:  0.004
CYP2C9-substrate:  0.283
CYP2D6-inhibitor:  0.004
CYP2D6-substrate:  0.295
CYP3A4-inhibitor:  0.005
CYP3A4-substrate:  0.171

ADMET: Excretion

Clearance (CL):  5.29
Half-life (T1/2):  0.837

ADMET: Toxicity

hERG Blockers:  0.025
Human Hepatotoxicity (H-HT):  0.058
Drug-inuced Liver Injury (DILI):  0.087
AMES Toxicity:  0.019
Rat Oral Acute Toxicity:  0.013
Maximum Recommended Daily Dose:  0.017
Skin Sensitization:  0.178
Carcinogencity:  0.01
Eye Corrosion:  0.632
Eye Irritation:  0.983
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: NPC325165

Natural Product ID:  NPC325165
Common Name*:   Methyl 2-Hydroxypropanoate
IUPAC Name:   methyl 2-hydroxypropanoate
Synonyms:  
Standard InCHIKey:  LPEKGGXMPWTOCB-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C4H8O3/c1-3(5)4(6)7-2/h3,5H,1-2H3
SMILES:  COC(=O)C(O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3183351
PubChem CID:   11040
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
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. fruit n.a. PMID[11312782]
NPO17024 Vitis vinifera Species Vitaceae Eukaryota n.a. leaf 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 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 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 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. 27890.2 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 2235.8 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 176 nM PubChem BioAssay data set
NPT2 Others Unspecified Potency n.a. 12572.6 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 NPC325165 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
0.9697 High Similarity NPC24967
0.9697 High Similarity NPC103612
0.8571 High Similarity NPC5505
0.8485 Intermediate Similarity NPC76217
0.8485 Intermediate Similarity NPC307739
0.7895 Intermediate Similarity NPC222792
0.7895 Intermediate Similarity NPC316217
0.7576 Intermediate Similarity NPC88135
0.7576 Intermediate Similarity NPC316272
0.7429 Intermediate Similarity NPC212144
0.7353 Intermediate Similarity NPC270334
0.7273 Intermediate Similarity NPC272307
0.7188 Intermediate Similarity NPC165122
0.7143 Intermediate Similarity NPC319680
0.7143 Intermediate Similarity NPC5934
0.7105 Intermediate Similarity NPC159089
0.7073 Intermediate Similarity NPC35661
0.697 Remote Similarity NPC127134
0.6944 Remote Similarity NPC281883
0.6857 Remote Similarity NPC232172
0.6842 Remote Similarity NPC191084
0.6842 Remote Similarity NPC250870
0.6842 Remote Similarity NPC168052
0.6667 Remote Similarity NPC97444
0.6667 Remote Similarity NPC19044
0.6667 Remote Similarity NPC100742
0.6667 Remote Similarity NPC121018
0.6667 Remote Similarity NPC41485
0.6667 Remote Similarity NPC24751
0.6667 Remote Similarity NPC192402
0.6667 Remote Similarity NPC140389
0.6667 Remote Similarity NPC32280
0.6667 Remote Similarity NPC304786
0.6591 Remote Similarity NPC242655
0.6591 Remote Similarity NPC38891
0.6579 Remote Similarity NPC140229
0.6562 Remote Similarity NPC8187
0.6512 Remote Similarity NPC144829
0.6486 Remote Similarity NPC261351
0.6471 Remote Similarity NPC166804
0.6471 Remote Similarity NPC128335
0.6471 Remote Similarity NPC286233
0.6429 Remote Similarity NPC320331
0.6389 Remote Similarity NPC292641
0.6364 Remote Similarity NPC110107
0.6364 Remote Similarity NPC318912
0.6364 Remote Similarity NPC318951
0.6364 Remote Similarity NPC237965
0.6364 Remote Similarity NPC114270
0.6286 Remote Similarity NPC143211
0.6279 Remote Similarity NPC322956
0.6279 Remote Similarity NPC325307
0.625 Remote Similarity NPC313405
0.6216 Remote Similarity NPC198126
0.6176 Remote Similarity NPC35155
0.6176 Remote Similarity NPC3693
0.6176 Remote Similarity NPC28246
0.6154 Remote Similarity NPC127142
0.6154 Remote Similarity NPC307027
0.6111 Remote Similarity NPC238135
0.6061 Remote Similarity NPC23508
0.6061 Remote Similarity NPC203105
0.6047 Remote Similarity NPC203382
0.6042 Remote Similarity NPC46254
0.6042 Remote Similarity NPC328954
0.6 Remote Similarity NPC201132
0.6 Remote Similarity NPC314668
0.6 Remote Similarity NPC149209
0.6 Remote Similarity NPC230726
0.6 Remote Similarity NPC320624
0.6 Remote Similarity NPC317724
0.6 Remote Similarity NPC316685
0.5946 Remote Similarity NPC127696
0.5897 Remote Similarity NPC217218
0.5882 Remote Similarity NPC327103
0.5882 Remote Similarity NPC157340
0.5854 Remote Similarity NPC321699
0.5833 Remote Similarity NPC320326
0.5833 Remote Similarity NPC248233
0.5814 Remote Similarity NPC225963
0.5814 Remote Similarity NPC474205
0.5789 Remote Similarity NPC21374
0.5789 Remote Similarity NPC302611
0.5789 Remote Similarity NPC265882
0.5778 Remote Similarity NPC259982
0.5778 Remote Similarity NPC228782
0.5778 Remote Similarity NPC313565
0.5769 Remote Similarity NPC320588
0.5769 Remote Similarity NPC23155
0.5769 Remote Similarity NPC53463
0.5769 Remote Similarity NPC469937
0.5758 Remote Similarity NPC299484
0.5758 Remote Similarity NPC181153
0.575 Remote Similarity NPC227267
0.5741 Remote Similarity NPC293692
0.5741 Remote Similarity NPC220922
0.5714 Remote Similarity NPC477778
0.5714 Remote Similarity NPC88887
0.5714 Remote Similarity NPC26253
0.5714 Remote Similarity NPC82694
0.5714 Remote Similarity NPC109026
0.5686 Remote Similarity NPC277878
0.5676 Remote Similarity NPC55956
0.5676 Remote Similarity NPC301586
0.5676 Remote Similarity NPC317739
0.5676 Remote Similarity NPC33415
0.5676 Remote Similarity NPC281943
0.5641 Remote Similarity NPC329270
0.5641 Remote Similarity NPC12904
0.5625 Remote Similarity NPC163707
0.561 Remote Similarity NPC317203

  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 NPC325165 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
0.875 High Similarity NPD54 Approved
0.875 High Similarity NPD8203 Approved
0.875 High Similarity NPD8206 Approved
0.875 High Similarity NPD8204 Approved
0.875 High Similarity NPD55 Approved
0.8485 Intermediate Similarity NPD8205 Approved
0.8485 Intermediate Similarity NPD8202 Approved
0.7143 Intermediate Similarity NPD8856 Phase 2
0.697 Remote Similarity NPD8989 Approved
0.6944 Remote Similarity NPD9636 Phase 2
0.6667 Remote Similarity NPD8598 Approved
0.6667 Remote Similarity NPD8604 Approved
0.6667 Remote Similarity NPD8605 Approved
0.6667 Remote Similarity NPD8600 Approved
0.6667 Remote Similarity NPD8601 Approved
0.6667 Remote Similarity NPD8603 Approved
0.6667 Remote Similarity NPD8602 Approved
0.6667 Remote Similarity NPD8599 Approved
0.6471 Remote Similarity NPD8189 Approved
0.6364 Remote Similarity NPD8225 Phase 3
0.6216 Remote Similarity NPD8618 Approved
0.6098 Remote Similarity NPD9131 Discovery
0.5946 Remote Similarity NPD8619 Approved
0.5946 Remote Similarity NPD8617 Approved
0.5882 Remote Similarity NPD8226 Approved
0.5769 Remote Similarity NPD3728 Approved
0.5769 Remote Similarity NPD3730 Approved
0.5758 Remote Similarity NPD8190 Phase 2
0.5758 Remote Similarity NPD8201 Phase 2
0.5741 Remote Similarity NPD8959 Approved
0.5714 Remote Similarity NPD8207 Approved
0.5686 Remote Similarity NPD72 Approved
0.5686 Remote Similarity NPD9011 Approved
0.5686 Remote Similarity NPD9008 Approved
0.5686 Remote Similarity NPD64 Approved
0.5686 Remote Similarity NPD9010 Approved
0.5686 Remote Similarity NPD9009 Approved
0.5686 Remote Similarity NPD65 Approved
0.5686 Remote Similarity NPD9007 Approved
0.5686 Remote Similarity NPD66 Approved
0.5686 Remote Similarity NPD8960 Approved
0.5676 Remote Similarity NPD8549 Clinical (unspecified phase)
0.5636 Remote Similarity NPD6109 Phase 1
0.5625 Remote Similarity NPD7356 Approved
0.5625 Remote Similarity NPD8224 Approved
0.5625 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