Structure

Physi-Chem Properties

Molecular Weight:  104.05
Volume:  101.475
LogP:  -0.728
LogD:  -1.282
LogS:  0.701
# Rotatable Bonds:  2
TPSA:  57.53
# H-Bond Aceptor:  3
# H-Bond Donor:  2
# Rings:  0
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.512
Synthetic Accessibility Score:  2.629
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:  -5.45
MDCK Permeability:  0.0037193128373473883
Pgp-inhibitor:  0.0
Pgp-substrate:  0.012
Human Intestinal Absorption (HIA):  0.017
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.795

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.917
Plasma Protein Binding (PPB):  9.535287857055664%
Volume Distribution (VD):  0.25
Pgp-substrate:  78.77519989013672%

ADMET: Metabolism

CYP1A2-inhibitor:  0.013
CYP1A2-substrate:  0.087
CYP2C19-inhibitor:  0.026
CYP2C19-substrate:  0.09
CYP2C9-inhibitor:  0.004
CYP2C9-substrate:  0.913
CYP2D6-inhibitor:  0.012
CYP2D6-substrate:  0.193
CYP3A4-inhibitor:  0.008
CYP3A4-substrate:  0.047

ADMET: Excretion

Clearance (CL):  6.902
Half-life (T1/2):  0.809

ADMET: Toxicity

hERG Blockers:  0.008
Human Hepatotoxicity (H-HT):  0.164
Drug-inuced Liver Injury (DILI):  0.047
AMES Toxicity:  0.019
Rat Oral Acute Toxicity:  0.026
Maximum Recommended Daily Dose:  0.025
Skin Sensitization:  0.165
Carcinogencity:  0.044
Eye Corrosion:  0.955
Eye Irritation:  0.991
Respiratory Toxicity:  0.036

Download Data

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

  Natural Product: NPC168052

Natural Product ID:  NPC168052
Common Name*:   3-Hydroxybutanoate
IUPAC Name:   3-hydroxybutanoic acid
Synonyms:   3-Hydroxybutanoate
Standard InCHIKey:  WHBMMWSBFZVSSR-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C4H8O3/c1-3(5)2-4(6)7/h3,5H,2H2,1H3,(H,6,7)
SMILES:  CC(CC(=O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1162496
PubChem CID:   441
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000472] Hydroxy acids and derivatives
        • [CHEMONTID:0001713] Beta hydroxy acids and derivatives

*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
NPT661 Individual Protein Solute carrier family 22 member 6 Mus musculus Ki = 3235936.57 nM PMID[568260]
NPT661 Individual Protein Solute carrier family 22 member 6 Mus musculus Ki = 3220000.0 nM PMID[568260]
NPT662 Individual Protein Solute carrier family 22 member 20 Mus musculus Ki = 190546.07 nM PMID[568260]
NPT662 Individual Protein Solute carrier family 22 member 20 Mus musculus Ki = 191000.0 nM PMID[568260]
NPT1632 Individual Protein Monocarboxylate transporter 2 Rattus norvegicus Ki = 1200000.0 nM PMID[568265]
NPT4908 Individual Protein Protein skinhead-1 Caenorhabditis elegans IC50 > 100000.0 nM PMID[568261]
NPT2 Others Unspecified Ratio pKi = 1.23 n.a. PMID[568260]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum Potency n.a. 3294.4 nM PMID[568261]
NPT706 Individual Protein Monocarboxylate transporter 1 Rattus norvegicus Activity = 20.0 % PMID[568263]
NPT873 Individual Protein Monocarboxylate transporter 2 Homo sapiens Activity = 30.0 % PMID[568263]
NPT706 Individual Protein Monocarboxylate transporter 1 Rattus norvegicus Activity = 7.0 % PMID[568264]
NPT2 Others Unspecified Potency n.a. 1122.0 nM PMID[568261]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 Inhibition = -2.14 % PMID[568269]
NPT20556 SINGLE PROTEIN Replicase polyprotein 1ab Severe acute respiratory syndrome coronavirus 2 Inhibition = 14.59 % PMID[568270]
NPT20555 ORGANISM SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 Inhibition = 0.01 % PMID[568271]

☑ 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 NPC168052 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 NPC250870
1.0 High Similarity NPC191084
0.8056 Intermediate Similarity NPC5505
0.7949 Intermediate Similarity NPC35661
0.7647 Intermediate Similarity NPC198126
0.7647 Intermediate Similarity NPC320981
0.75 Intermediate Similarity NPC121018
0.75 Intermediate Similarity NPC100742
0.75 Intermediate Similarity NPC192402
0.75 Intermediate Similarity NPC97444
0.75 Intermediate Similarity NPC24751
0.75 Intermediate Similarity NPC19044
0.75 Intermediate Similarity NPC149209
0.7436 Intermediate Similarity NPC316217
0.7436 Intermediate Similarity NPC222792
0.7297 Intermediate Similarity NPC316685
0.7273 Intermediate Similarity NPC200618
0.7273 Intermediate Similarity NPC131770
0.7222 Intermediate Similarity NPC217218
0.7188 Intermediate Similarity NPC88887
0.7143 Intermediate Similarity NPC302611
0.7111 Intermediate Similarity NPC93888
0.7111 Intermediate Similarity NPC270805
0.7105 Intermediate Similarity NPC159089
0.6957 Remote Similarity NPC295832
0.6957 Remote Similarity NPC90904
0.6957 Remote Similarity NPC27359
0.6957 Remote Similarity NPC198398
0.6944 Remote Similarity NPC328569
0.6944 Remote Similarity NPC307739
0.6944 Remote Similarity NPC76217
0.6889 Remote Similarity NPC327542
0.6857 Remote Similarity NPC151140
0.6857 Remote Similarity NPC122768
0.6857 Remote Similarity NPC61066
0.6857 Remote Similarity NPC174368
0.6857 Remote Similarity NPC270334
0.6857 Remote Similarity NPC292641
0.6857 Remote Similarity NPC104195
0.6842 Remote Similarity NPC325165
0.6842 Remote Similarity NPC317203
0.6829 Remote Similarity NPC320331
0.6818 Remote Similarity NPC133771
0.6765 Remote Similarity NPC143211
0.6744 Remote Similarity NPC319680
0.6739 Remote Similarity NPC328954
0.6739 Remote Similarity NPC46254
0.6667 Remote Similarity NPC474361
0.6667 Remote Similarity NPC265882
0.6667 Remote Similarity NPC103612
0.6667 Remote Similarity NPC28246
0.6667 Remote Similarity NPC24967
0.6667 Remote Similarity NPC241404
0.6579 Remote Similarity NPC307027
0.6579 Remote Similarity NPC7814
0.6579 Remote Similarity NPC127142
0.6571 Remote Similarity NPC55956
0.6512 Remote Similarity NPC310220
0.6512 Remote Similarity NPC259982
0.6512 Remote Similarity NPC228782
0.6512 Remote Similarity NPC313565
0.6486 Remote Similarity NPC280532
0.6471 Remote Similarity NPC3343
0.6471 Remote Similarity NPC314668
0.6471 Remote Similarity NPC166804
0.6471 Remote Similarity NPC127134
0.6471 Remote Similarity NPC230726
0.6364 Remote Similarity NPC245688
0.6327 Remote Similarity NPC277878
0.6316 Remote Similarity NPC94196
0.6316 Remote Similarity NPC175342
0.6304 Remote Similarity NPC324004
0.6304 Remote Similarity NPC328497
0.6286 Remote Similarity NPC320326
0.6279 Remote Similarity NPC322956
0.6279 Remote Similarity NPC325307
0.625 Remote Similarity NPC1037
0.625 Remote Similarity NPC321699
0.625 Remote Similarity NPC181153
0.625 Remote Similarity NPC299484
0.6222 Remote Similarity NPC38891
0.6222 Remote Similarity NPC242655
0.6222 Remote Similarity NPC270088
0.6216 Remote Similarity NPC21374
0.62 Remote Similarity NPC19676
0.62 Remote Similarity NPC196612
0.62 Remote Similarity NPC323401
0.6176 Remote Similarity NPC3693
0.6176 Remote Similarity NPC140389
0.6176 Remote Similarity NPC41485
0.6176 Remote Similarity NPC32280
0.6176 Remote Similarity NPC232554
0.617 Remote Similarity NPC106872
0.6136 Remote Similarity NPC107645
0.6111 Remote Similarity NPC33415
0.6111 Remote Similarity NPC301586
0.6111 Remote Similarity NPC88135
0.6111 Remote Similarity NPC236709
0.6098 Remote Similarity NPC109026
0.6098 Remote Similarity NPC206924
0.6078 Remote Similarity NPC6883
0.6061 Remote Similarity NPC39977
0.6061 Remote Similarity NPC8187
0.6053 Remote Similarity NPC12904
0.6053 Remote Similarity NPC261351
0.6053 Remote Similarity NPC281883
0.6053 Remote Similarity NPC212144
0.6042 Remote Similarity NPC304162
0.6 Remote Similarity NPC560
0.6 Remote Similarity NPC76051
0.6 Remote Similarity NPC318951
0.6 Remote Similarity NPC320624
0.6 Remote Similarity NPC286233
0.6 Remote Similarity NPC317680
0.5952 Remote Similarity NPC38930
0.5946 Remote Similarity NPC180423
0.5938 Remote Similarity NPC294703
0.5897 Remote Similarity NPC35371
0.5897 Remote Similarity NPC41007
0.5897 Remote Similarity NPC18224
0.5897 Remote Similarity NPC328710
0.5897 Remote Similarity NPC108238
0.5897 Remote Similarity NPC178643
0.5897 Remote Similarity NPC286695
0.5897 Remote Similarity NPC168714
0.5897 Remote Similarity NPC125575
0.5882 Remote Similarity NPC94144
0.5882 Remote Similarity NPC87529
0.5882 Remote Similarity NPC110107
0.5882 Remote Similarity NPC114270
0.5882 Remote Similarity NPC157340
0.5854 Remote Similarity NPC155263
0.5833 Remote Similarity NPC172086
0.5833 Remote Similarity NPC248233
0.5833 Remote Similarity NPC247546
0.5818 Remote Similarity NPC318306
0.5818 Remote Similarity NPC17935
0.5814 Remote Similarity NPC94368
0.5814 Remote Similarity NPC329545
0.58 Remote Similarity NPC470411
0.5789 Remote Similarity NPC5934
0.5769 Remote Similarity NPC469937
0.5769 Remote Similarity NPC23155
0.5769 Remote Similarity NPC320588
0.5769 Remote Similarity NPC53463
0.5758 Remote Similarity NPC219266
0.575 Remote Similarity NPC154396
0.5745 Remote Similarity NPC12438
0.5745 Remote Similarity NPC30195
0.5741 Remote Similarity NPC293692
0.5741 Remote Similarity NPC220922
0.5714 Remote Similarity NPC317945
0.5714 Remote Similarity NPC82694
0.5714 Remote Similarity NPC35155
0.5714 Remote Similarity NPC252843
0.5714 Remote Similarity NPC158179
0.5714 Remote Similarity NPC190797
0.5676 Remote Similarity NPC159845
0.5676 Remote Similarity NPC234005
0.5676 Remote Similarity NPC317739
0.5676 Remote Similarity NPC281943
0.5641 Remote Similarity NPC187058
0.5641 Remote Similarity NPC182541
0.5641 Remote Similarity NPC149070
0.5641 Remote Similarity NPC228727
0.5641 Remote Similarity NPC127074
0.5641 Remote Similarity NPC197207
0.5636 Remote Similarity NPC320032
0.5625 Remote Similarity NPC236761
0.5625 Remote Similarity NPC163707
0.56 Remote Similarity NPC473487

  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 NPC168052 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
0.7647 Intermediate Similarity NPD8590 Approved
0.7647 Intermediate Similarity NPD8618 Approved
0.75 Intermediate Similarity NPD8605 Approved
0.75 Intermediate Similarity NPD8604 Approved
0.75 Intermediate Similarity NPD8598 Approved
0.75 Intermediate Similarity NPD8601 Approved
0.75 Intermediate Similarity NPD8600 Approved
0.75 Intermediate Similarity NPD8602 Approved
0.75 Intermediate Similarity NPD8599 Approved
0.75 Intermediate Similarity NPD8603 Approved
0.7353 Intermediate Similarity NPD8617 Approved
0.7353 Intermediate Similarity NPD8619 Approved
0.7111 Intermediate Similarity NPD8624 Approved
0.6957 Remote Similarity NPD9226 Approved
0.6957 Remote Similarity NPD9225 Phase 3
0.6944 Remote Similarity NPD8205 Approved
0.6944 Remote Similarity NPD8202 Approved
0.6765 Remote Similarity NPD106 Approved
0.6667 Remote Similarity NPD8204 Approved
0.6667 Remote Similarity NPD8206 Approved
0.6667 Remote Similarity NPD55 Approved
0.6667 Remote Similarity NPD54 Approved
0.6667 Remote Similarity NPD8203 Approved
0.6579 Remote Similarity NPD8857 Approved
0.6471 Remote Similarity NPD8989 Approved
0.6327 Remote Similarity NPD9010 Approved
0.6327 Remote Similarity NPD9008 Approved
0.6327 Remote Similarity NPD65 Approved
0.6327 Remote Similarity NPD8960 Approved
0.6327 Remote Similarity NPD9011 Approved
0.6327 Remote Similarity NPD64 Approved
0.6327 Remote Similarity NPD72 Approved
0.6327 Remote Similarity NPD9009 Approved
0.6327 Remote Similarity NPD66 Approved
0.6327 Remote Similarity NPD9007 Approved
0.625 Remote Similarity NPD8616 Clinical (unspecified phase)
0.625 Remote Similarity NPD8201 Phase 2
0.625 Remote Similarity NPD8615 Phase 2
0.6111 Remote Similarity NPD8549 Clinical (unspecified phase)
0.6111 Remote Similarity NPD8594 Approved
0.6111 Remote Similarity NPD8593 Approved
0.6053 Remote Similarity NPD9636 Phase 2
0.6 Remote Similarity NPD8189 Approved
0.5962 Remote Similarity NPD9659 Approved
0.5909 Remote Similarity NPD9116 Phase 1
0.5882 Remote Similarity NPD8226 Approved
0.5882 Remote Similarity NPD8225 Phase 3
0.5849 Remote Similarity NPD73 Approved
0.5833 Remote Similarity NPD9005 Phase 3
0.5833 Remote Similarity NPD9003 Clinical (unspecified phase)
0.5833 Remote Similarity NPD9004 Approved
0.5833 Remote Similarity NPD8990 Clinical (unspecified phase)
0.5789 Remote Similarity NPD8856 Phase 2
0.5769 Remote Similarity NPD3728 Approved
0.5769 Remote Similarity NPD3730 Approved
0.575 Remote Similarity NPD900 Approved
0.5741 Remote Similarity NPD8959 Approved
0.5714 Remote Similarity NPD8188 Approved
0.5714 Remote Similarity NPD8964 Approved
0.5714 Remote Similarity NPD8207 Approved
0.5641 Remote Similarity NPD8814 Phase 3
0.5625 Remote Similarity NPD8224 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