Structure

Physi-Chem Properties

Molecular Weight:  118.06
Volume:  118.771
LogP:  0.055
LogD:  0.143
LogS:  0.558
# Rotatable Bonds:  3
TPSA:  46.53
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.516
Synthetic Accessibility Score:  2.503
Fsp3:  0.8
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:  -4.326
MDCK Permeability:  0.0005941459094174206
Pgp-inhibitor:  0.0
Pgp-substrate:  0.004
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.01
30% Bioavailability (F30%):  0.899

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.782
Plasma Protein Binding (PPB):  7.041085243225098%
Volume Distribution (VD):  0.908
Pgp-substrate:  86.28560638427734%

ADMET: Metabolism

CYP1A2-inhibitor:  0.231
CYP1A2-substrate:  0.348
CYP2C19-inhibitor:  0.046
CYP2C19-substrate:  0.765
CYP2C9-inhibitor:  0.007
CYP2C9-substrate:  0.36
CYP2D6-inhibitor:  0.005
CYP2D6-substrate:  0.265
CYP3A4-inhibitor:  0.005
CYP3A4-substrate:  0.234

ADMET: Excretion

Clearance (CL):  5.857
Half-life (T1/2):  0.803

ADMET: Toxicity

hERG Blockers:  0.038
Human Hepatotoxicity (H-HT):  0.016
Drug-inuced Liver Injury (DILI):  0.099
AMES Toxicity:  0.018
Rat Oral Acute Toxicity:  0.008
Maximum Recommended Daily Dose:  0.01
Skin Sensitization:  0.184
Carcinogencity:  0.012
Eye Corrosion:  0.653
Eye Irritation:  0.985
Respiratory Toxicity:  0.072

Download Data

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

  Natural Product: NPC103612

Natural Product ID:  NPC103612
Common Name*:   Ethyl (2S)-2-Hydroxypropanoate
IUPAC Name:   ethyl (2S)-2-hydroxypropanoate
Synonyms:  
Standard InCHIKey:  LZCLXQDLBQLTDK-BYPYZUCNSA-N
Standard InCHI:  InChI=1S/C5H10O3/c1-3-8-5(7)4(2)6/h4,6H,3H2,1-2H3/t4-/m0/s1
SMILES:  CCOC(=O)[C@@H](O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3560966
PubChem CID:   92831
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
NPO17823 Lycium chinense Species Solanaceae Eukaryota fruits n.a. n.a. PMID[12467621]
NPO17823 Lycium chinense Species Solanaceae Eukaryota n.a. root n.a. PMID[16212233]
NPO17823 Lycium chinense Species Solanaceae Eukaryota root bark n.a. n.a. PMID[23282106]
NPO17823 Lycium chinense Species Solanaceae Eukaryota Root Bark n.a. n.a. PMID[26982999]
NPO23429 Lycium barbarum Species Solanaceae Eukaryota n.a. n.a. n.a. PMID[31397570]
NPO17823 Lycium chinense Species Solanaceae Eukaryota fruits n.a. n.a. PMID[9090870]
NPO17823 Lycium chinense Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO23429 Lycium barbarum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO17823 Lycium chinense Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23429 Lycium barbarum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23429 Lycium barbarum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO17823 Lycium chinense Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO23429 Lycium barbarum Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO17823 Lycium chinense Species Solanaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO17823 Lycium chinense Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23429 Lycium barbarum Species Solanaceae 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. 2.8 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 NPC103612 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 NPC24967
0.9697 High Similarity NPC325165
0.8333 Intermediate Similarity NPC5505
0.8235 Intermediate Similarity NPC76217
0.8235 Intermediate Similarity NPC307739
0.7879 Intermediate Similarity NPC88135
0.7692 Intermediate Similarity NPC222792
0.7692 Intermediate Similarity NPC316217
0.7576 Intermediate Similarity NPC272307
0.7429 Intermediate Similarity NPC5934
0.7353 Intermediate Similarity NPC316272
0.7273 Intermediate Similarity NPC127134
0.7222 Intermediate Similarity NPC281883
0.7222 Intermediate Similarity NPC212144
0.7143 Intermediate Similarity NPC232172
0.7143 Intermediate Similarity NPC270334
0.6977 Remote Similarity NPC319680
0.697 Remote Similarity NPC165122
0.697 Remote Similarity NPC41485
0.697 Remote Similarity NPC304786
0.697 Remote Similarity NPC32280
0.6923 Remote Similarity NPC159089
0.6905 Remote Similarity NPC35661
0.6842 Remote Similarity NPC140229
0.6765 Remote Similarity NPC166804
0.6765 Remote Similarity NPC128335
0.6744 Remote Similarity NPC144829
0.6667 Remote Similarity NPC191084
0.6667 Remote Similarity NPC110107
0.6667 Remote Similarity NPC318912
0.6667 Remote Similarity NPC168052
0.6667 Remote Similarity NPC250870
0.6667 Remote Similarity NPC237965
0.6571 Remote Similarity NPC143211
0.6512 Remote Similarity NPC24751
0.6512 Remote Similarity NPC19044
0.6512 Remote Similarity NPC100742
0.6512 Remote Similarity NPC97444
0.6512 Remote Similarity NPC121018
0.6512 Remote Similarity NPC192402
0.65 Remote Similarity NPC313405
0.6471 Remote Similarity NPC140389
0.6471 Remote Similarity NPC3693
0.6444 Remote Similarity NPC38891
0.6444 Remote Similarity NPC242655
0.6389 Remote Similarity NPC238135
0.6364 Remote Similarity NPC203105
0.6364 Remote Similarity NPC23508
0.6364 Remote Similarity NPC8187
0.6316 Remote Similarity NPC261351
0.6286 Remote Similarity NPC201132
0.6286 Remote Similarity NPC317724
0.6286 Remote Similarity NPC286233
0.6279 Remote Similarity NPC320331
0.6279 Remote Similarity NPC203382
0.625 Remote Similarity NPC46254
0.6222 Remote Similarity NPC318951
0.6216 Remote Similarity NPC292641
0.6216 Remote Similarity NPC127696
0.6176 Remote Similarity NPC114270
0.6154 Remote Similarity NPC217218
0.6136 Remote Similarity NPC325307
0.6136 Remote Similarity NPC322956
0.6111 Remote Similarity NPC248233
0.6098 Remote Similarity NPC321699
0.6078 Remote Similarity NPC327103
0.6053 Remote Similarity NPC198126
0.6053 Remote Similarity NPC21374
0.6053 Remote Similarity NPC265882
0.6047 Remote Similarity NPC225963
0.6047 Remote Similarity NPC474205
0.6 Remote Similarity NPC307027
0.6 Remote Similarity NPC28246
0.6 Remote Similarity NPC35155
0.6 Remote Similarity NPC127142
0.6 Remote Similarity NPC227267
0.5962 Remote Similarity NPC23155
0.5962 Remote Similarity NPC469937
0.5962 Remote Similarity NPC53463
0.5962 Remote Similarity NPC320588
0.5946 Remote Similarity NPC281943
0.5946 Remote Similarity NPC317739
0.5926 Remote Similarity NPC220922
0.5926 Remote Similarity NPC293692
0.5918 Remote Similarity NPC26253
0.5918 Remote Similarity NPC328954
0.5918 Remote Similarity NPC477778
0.5897 Remote Similarity NPC12904
0.587 Remote Similarity NPC320624
0.5854 Remote Similarity NPC316685
0.5833 Remote Similarity NPC230452
0.5833 Remote Similarity NPC314668
0.5833 Remote Similarity NPC329496
0.5833 Remote Similarity NPC211250
0.5833 Remote Similarity NPC149209
0.5833 Remote Similarity NPC230726
0.575 Remote Similarity NPC286695
0.575 Remote Similarity NPC35371
0.575 Remote Similarity NPC108238
0.575 Remote Similarity NPC322892
0.575 Remote Similarity NPC41007
0.575 Remote Similarity NPC168714
0.575 Remote Similarity NPC178643
0.5745 Remote Similarity NPC51329
0.5741 Remote Similarity NPC198377
0.5714 Remote Similarity NPC157340
0.5714 Remote Similarity NPC233231
0.5686 Remote Similarity NPC287811
0.5682 Remote Similarity NPC94368
0.5676 Remote Similarity NPC320326
0.566 Remote Similarity NPC289979
0.5652 Remote Similarity NPC313565
0.5652 Remote Similarity NPC228782
0.5652 Remote Similarity NPC259982
0.5641 Remote Similarity NPC302611
0.561 Remote Similarity NPC154396

  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 NPC103612 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
0.8485 Intermediate Similarity NPD54 Approved
0.8485 Intermediate Similarity NPD8203 Approved
0.8485 Intermediate Similarity NPD8206 Approved
0.8485 Intermediate Similarity NPD55 Approved
0.8485 Intermediate Similarity NPD8204 Approved
0.8235 Intermediate Similarity NPD8205 Approved
0.8235 Intermediate Similarity NPD8202 Approved
0.7429 Intermediate Similarity NPD8856 Phase 2
0.7273 Intermediate Similarity NPD8989 Approved
0.7222 Intermediate Similarity NPD9636 Phase 2
0.6512 Remote Similarity NPD8604 Approved
0.6512 Remote Similarity NPD8598 Approved
0.6512 Remote Similarity NPD8599 Approved
0.6512 Remote Similarity NPD8601 Approved
0.6512 Remote Similarity NPD8603 Approved
0.6512 Remote Similarity NPD8605 Approved
0.6512 Remote Similarity NPD8600 Approved
0.6512 Remote Similarity NPD8602 Approved
0.6341 Remote Similarity NPD9131 Discovery
0.6286 Remote Similarity NPD8189 Approved
0.6176 Remote Similarity NPD8225 Phase 3
0.6053 Remote Similarity NPD8618 Approved
0.5962 Remote Similarity NPD3728 Approved
0.5962 Remote Similarity NPD3730 Approved
0.5926 Remote Similarity NPD8959 Approved
0.5818 Remote Similarity NPD6109 Phase 1
0.5789 Remote Similarity NPD8617 Approved
0.5789 Remote Similarity NPD8619 Approved
0.5778 Remote Similarity NPD8967 Approved
0.5714 Remote Similarity NPD8226 Approved
0.561 Remote Similarity NPD900 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