Structure

Physi-Chem Properties

Molecular Weight:  148.04
Volume:  133.715
LogP:  -1.651
LogD:  -1.52
LogS:  0.189
# Rotatable Bonds:  4
TPSA:  94.83
# H-Bond Aceptor:  5
# H-Bond Donor:  3
# Rings:  0
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.341
Synthetic Accessibility Score:  2.709
Fsp3:  0.6
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  2
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.984
MDCK Permeability:  0.007395938504487276
Pgp-inhibitor:  0.001
Pgp-substrate:  0.083
Human Intestinal Absorption (HIA):  0.981
20% Bioavailability (F20%):  0.993
30% Bioavailability (F30%):  0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.723
Plasma Protein Binding (PPB):  18.61712074279785%
Volume Distribution (VD):  0.282
Pgp-substrate:  76.714111328125%

ADMET: Metabolism

CYP1A2-inhibitor:  0.01
CYP1A2-substrate:  0.048
CYP2C19-inhibitor:  0.035
CYP2C19-substrate:  0.05
CYP2C9-inhibitor:  0.014
CYP2C9-substrate:  0.421
CYP2D6-inhibitor:  0.011
CYP2D6-substrate:  0.136
CYP3A4-inhibitor:  0.011
CYP3A4-substrate:  0.026

ADMET: Excretion

Clearance (CL):  3.079
Half-life (T1/2):  0.846

ADMET: Toxicity

hERG Blockers:  0.023
Human Hepatotoxicity (H-HT):  0.212
Drug-inuced Liver Injury (DILI):  0.109
AMES Toxicity:  0.029
Rat Oral Acute Toxicity:  0.004
Maximum Recommended Daily Dose:  0.017
Skin Sensitization:  0.304
Carcinogencity:  0.019
Eye Corrosion:  0.027
Eye Irritation:  0.979
Respiratory Toxicity:  0.315

Download Data

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

  Natural Product: NPC242655

Natural Product ID:  NPC242655
Common Name*:   L-2-Hydroxyglutarate
IUPAC Name:   (2S)-2-hydroxypentanedioic acid
Synonyms:   (S)-2-Hydroxypentanedioic Acid; L-2-Hydroxyglutarate
Standard InCHIKey:  HWXBTNAVRSUOJR-VKHMYHEASA-N
Standard InCHI:  InChI=1S/C5H8O5/c6-3(5(9)10)1-2-4(7)8/h3,6H,1-2H2,(H,7,8)(H,9,10)/t3-/m0/s1
SMILES:  C(CC(=O)O)[C@@H](C(=O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1615211
PubChem CID:   439939
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000472] Hydroxy acids and derivatives
        • [CHEMONTID:0000266] Short-chain 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 = 840000.0 nM PMID[549645]
NPT532 Individual Protein Lysine-specific demethylase 4A Homo sapiens IC50 = 26000.0 nM PMID[549646]
NPT2724 Individual Protein Lysine-specific demethylase 2A Homo sapiens IC50 = 48000.0 nM PMID[549646]
NPT2725 Individual Protein Lysine-specific demethylase 4C Homo sapiens IC50 = 97000.0 nM PMID[549646]
NPT1510 Individual Protein Alpha-ketoglutarate-dependent dioxygenase FTO Homo sapiens IC50 = 320000.0 nM PMID[549647]
NPT22599 SINGLE PROTEIN Prolyl 4-hydroxylase Paramecium bursaria Chlorella virus 1 IC50 > 500000.0 nM PMID[549648]

☑ 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 NPC242655 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 NPC38891
0.8367 Intermediate Similarity NPC19676
0.8367 Intermediate Similarity NPC323401
0.82 Intermediate Similarity NPC6883
0.8163 Intermediate Similarity NPC277878
0.8 Intermediate Similarity NPC196612
0.7955 Intermediate Similarity NPC35661
0.7826 Intermediate Similarity NPC270088
0.7778 Intermediate Similarity NPC259982
0.7778 Intermediate Similarity NPC313565
0.7778 Intermediate Similarity NPC228782
0.7708 Intermediate Similarity NPC172086
0.7708 Intermediate Similarity NPC247546
0.7674 Intermediate Similarity NPC128713
0.7619 Intermediate Similarity NPC5505
0.7609 Intermediate Similarity NPC319680
0.7556 Intermediate Similarity NPC97444
0.7556 Intermediate Similarity NPC100742
0.7556 Intermediate Similarity NPC192402
0.7556 Intermediate Similarity NPC19044
0.7556 Intermediate Similarity NPC24751
0.7556 Intermediate Similarity NPC121018
0.7551 Intermediate Similarity NPC293378
0.7551 Intermediate Similarity NPC46254
0.7407 Intermediate Similarity NPC220922
0.7407 Intermediate Similarity NPC293692
0.7333 Intermediate Similarity NPC320331
0.7317 Intermediate Similarity NPC125575
0.7308 Intermediate Similarity NPC65985
0.7222 Intermediate Similarity NPC198377
0.7143 Intermediate Similarity NPC323945
0.7111 Intermediate Similarity NPC222792
0.7111 Intermediate Similarity NPC316217
0.7091 Intermediate Similarity NPC61567
0.7069 Intermediate Similarity NPC88898
0.7069 Intermediate Similarity NPC106216
0.7045 Intermediate Similarity NPC206924
0.7037 Intermediate Similarity NPC60830
0.7037 Intermediate Similarity NPC68743
0.7018 Intermediate Similarity NPC320296
0.6964 Remote Similarity NPC179624
0.6957 Remote Similarity NPC240109
0.6863 Remote Similarity NPC328954
0.6829 Remote Similarity NPC198126
0.678 Remote Similarity NPC258690
0.678 Remote Similarity NPC317651
0.6744 Remote Similarity NPC127142
0.6667 Remote Similarity NPC76217
0.6667 Remote Similarity NPC317945
0.6667 Remote Similarity NPC307739
0.6667 Remote Similarity NPC149070
0.6667 Remote Similarity NPC187058
0.6667 Remote Similarity NPC197207
0.6667 Remote Similarity NPC182541
0.6667 Remote Similarity NPC127074
0.6607 Remote Similarity NPC3547
0.6591 Remote Similarity NPC317203
0.6591 Remote Similarity NPC325165
0.6522 Remote Similarity NPC325454
0.6444 Remote Similarity NPC24967
0.6444 Remote Similarity NPC159089
0.6444 Remote Similarity NPC103612
0.6364 Remote Similarity NPC7814
0.6349 Remote Similarity NPC57788
0.6349 Remote Similarity NPC32148
0.6349 Remote Similarity NPC53879
0.6327 Remote Similarity NPC310220
0.6304 Remote Similarity NPC109026
0.6296 Remote Similarity NPC100096
0.6222 Remote Similarity NPC293908
0.6222 Remote Similarity NPC250870
0.6222 Remote Similarity NPC191084
0.6222 Remote Similarity NPC66052
0.6222 Remote Similarity NPC325034
0.6222 Remote Similarity NPC86412
0.6222 Remote Similarity NPC316685
0.6222 Remote Similarity NPC192065
0.6222 Remote Similarity NPC168052
0.619 Remote Similarity NPC174368
0.617 Remote Similarity NPC38930
0.6136 Remote Similarity NPC328710
0.6136 Remote Similarity NPC18224
0.6087 Remote Similarity NPC321699
0.6087 Remote Similarity NPC1037
0.6 Remote Similarity NPC17935
0.5965 Remote Similarity NPC23155
0.5965 Remote Similarity NPC53463
0.5965 Remote Similarity NPC469937
0.5965 Remote Similarity NPC320588
0.5952 Remote Similarity NPC33415
0.5952 Remote Similarity NPC236709
0.5952 Remote Similarity NPC301586
0.5909 Remote Similarity NPC212144
0.5849 Remote Similarity NPC324004
0.5849 Remote Similarity NPC328497
0.5833 Remote Similarity NPC322855
0.5814 Remote Similarity NPC270334
0.5814 Remote Similarity NPC292641
0.58 Remote Similarity NPC325307
0.58 Remote Similarity NPC322956
0.5778 Remote Similarity NPC99700
0.5778 Remote Similarity NPC175342
0.5745 Remote Similarity NPC134782
0.5741 Remote Similarity NPC200618
0.5741 Remote Similarity NPC131770
0.5741 Remote Similarity NPC106872
0.5714 Remote Similarity NPC268243
0.5714 Remote Similarity NPC325773
0.5714 Remote Similarity NPC320326
0.5714 Remote Similarity NPC94368
0.5692 Remote Similarity NPC241949
0.5686 Remote Similarity NPC213159
0.5686 Remote Similarity NPC86191
0.5686 Remote Similarity NPC317182
0.5686 Remote Similarity NPC291502
0.5686 Remote Similarity NPC298699
0.5686 Remote Similarity NPC320189
0.5686 Remote Similarity NPC134252
0.5686 Remote Similarity NPC289686
0.5672 Remote Similarity NPC28526
0.5667 Remote Similarity NPC43169
0.5667 Remote Similarity NPC93861
0.5667 Remote Similarity NPC327895
0.5667 Remote Similarity NPC112224
0.5667 Remote Similarity NPC323436
0.566 Remote Similarity NPC133771
0.5652 Remote Similarity NPC227267
0.5652 Remote Similarity NPC307027
0.5636 Remote Similarity NPC304162
0.5614 Remote Similarity NPC317680
0.561 Remote Similarity NPC165122
0.56 Remote Similarity NPC88278
0.56 Remote Similarity NPC227707
0.56 Remote Similarity NPC111882
0.56 Remote Similarity NPC266553
0.56 Remote Similarity NPC102981
0.56 Remote Similarity NPC99573

  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 NPC242655 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
0.8163 Intermediate Similarity NPD66 Approved
0.8163 Intermediate Similarity NPD64 Approved
0.8163 Intermediate Similarity NPD8960 Approved
0.8163 Intermediate Similarity NPD9011 Approved
0.8163 Intermediate Similarity NPD9008 Approved
0.8163 Intermediate Similarity NPD72 Approved
0.8163 Intermediate Similarity NPD65 Approved
0.8163 Intermediate Similarity NPD9007 Approved
0.8163 Intermediate Similarity NPD9010 Approved
0.8163 Intermediate Similarity NPD9009 Approved
0.7708 Intermediate Similarity NPD9005 Phase 3
0.7708 Intermediate Similarity NPD9003 Clinical (unspecified phase)
0.7708 Intermediate Similarity NPD9004 Approved
0.7556 Intermediate Similarity NPD8599 Approved
0.7556 Intermediate Similarity NPD8604 Approved
0.7556 Intermediate Similarity NPD8598 Approved
0.7556 Intermediate Similarity NPD8600 Approved
0.7556 Intermediate Similarity NPD8601 Approved
0.7556 Intermediate Similarity NPD8605 Approved
0.7556 Intermediate Similarity NPD8603 Approved
0.7556 Intermediate Similarity NPD8602 Approved
0.7551 Intermediate Similarity NPD9129 Approved
0.7551 Intermediate Similarity NPD9126 Approved
0.7551 Intermediate Similarity NPD71 Approved
0.7547 Intermediate Similarity NPD73 Approved
0.7407 Intermediate Similarity NPD8959 Approved
0.7347 Intermediate Similarity NPD9125 Approved
0.7347 Intermediate Similarity NPD9123 Approved
0.7347 Intermediate Similarity NPD9127 Approved
0.7347 Intermediate Similarity NPD9128 Approved
0.7347 Intermediate Similarity NPD109 Approved
0.7347 Intermediate Similarity NPD9130 Phase 3
0.7347 Intermediate Similarity NPD9121 Approved
0.7347 Intermediate Similarity NPD9124 Approved
0.7347 Intermediate Similarity NPD70 Approved
0.7347 Intermediate Similarity NPD108 Approved
0.7347 Intermediate Similarity NPD9122 Approved
0.7255 Intermediate Similarity NPD9002 Approved
0.7255 Intermediate Similarity NPD9001 Clinical (unspecified phase)
0.6829 Remote Similarity NPD8618 Approved
0.678 Remote Similarity NPD8961 Approved
0.6667 Remote Similarity NPD8202 Approved
0.6667 Remote Similarity NPD8205 Approved
0.6667 Remote Similarity NPD8814 Phase 3
0.6585 Remote Similarity NPD8619 Approved
0.6585 Remote Similarity NPD8617 Approved
0.6538 Remote Similarity NPD8964 Approved
0.6429 Remote Similarity NPD8203 Approved
0.6429 Remote Similarity NPD54 Approved
0.6429 Remote Similarity NPD8204 Approved
0.6429 Remote Similarity NPD8206 Approved
0.6429 Remote Similarity NPD55 Approved
0.6364 Remote Similarity NPD8857 Approved
0.6349 Remote Similarity NPD898 Approved
0.6349 Remote Similarity NPD896 Approved
0.6349 Remote Similarity NPD897 Approved
0.6222 Remote Similarity NPD9053 Approved
0.6222 Remote Similarity NPD9051 Approved
0.6222 Remote Similarity NPD9052 Approved
0.5965 Remote Similarity NPD3728 Approved
0.5965 Remote Similarity NPD3730 Approved
0.5952 Remote Similarity NPD8593 Approved
0.5952 Remote Similarity NPD8549 Clinical (unspecified phase)
0.5952 Remote Similarity NPD8594 Approved
0.5902 Remote Similarity NPD9120 Clinical (unspecified phase)
0.5882 Remote Similarity NPD8975 Clinical (unspecified phase)
0.5873 Remote Similarity NPD7909 Approved
0.5769 Remote Similarity NPD8974 Clinical (unspecified phase)
0.5714 Remote Similarity NPD11 Approved
0.5714 Remote Similarity NPD376 Approved
0.5686 Remote Similarity NPD8788 Approved
0.56 Remote Similarity NPD8995 Clinical (unspecified phase)
0.56 Remote Similarity NPD8996 Phase 3

  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