Structure

Physi-Chem Properties

Molecular Weight:  190.01
Volume:  157.398
LogP:  -0.325
LogD:  -0.545
LogS:  -0.504
# Rotatable Bonds:  2
TPSA:  121.13
# H-Bond Aceptor:  7
# H-Bond Donor:  3
# Rings:  1
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.439
Synthetic Accessibility Score:  3.919
Fsp3:  0.5
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:  -6.139
MDCK Permeability:  0.0015824859729036689
Pgp-inhibitor:  0.0
Pgp-substrate:  0.522
Human Intestinal Absorption (HIA):  0.029
20% Bioavailability (F20%):  0.009
30% Bioavailability (F30%):  0.216

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.348
Plasma Protein Binding (PPB):  15.375100135803223%
Volume Distribution (VD):  0.281
Pgp-substrate:  72.71573638916016%

ADMET: Metabolism

CYP1A2-inhibitor:  0.003
CYP1A2-substrate:  0.061
CYP2C19-inhibitor:  0.02
CYP2C19-substrate:  0.041
CYP2C9-inhibitor:  0.002
CYP2C9-substrate:  0.349
CYP2D6-inhibitor:  0.014
CYP2D6-substrate:  0.094
CYP3A4-inhibitor:  0.022
CYP3A4-substrate:  0.005

ADMET: Excretion

Clearance (CL):  2.176
Half-life (T1/2):  0.727

ADMET: Toxicity

hERG Blockers:  0.014
Human Hepatotoxicity (H-HT):  0.038
Drug-inuced Liver Injury (DILI):  0.427
AMES Toxicity:  0.037
Rat Oral Acute Toxicity:  0.011
Maximum Recommended Daily Dose:  0.002
Skin Sensitization:  0.522
Carcinogencity:  0.014
Eye Corrosion:  0.998
Eye Irritation:  0.96
Respiratory Toxicity:  0.037

Download Data

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

  Natural Product: NPC61567

Natural Product ID:  NPC61567
Common Name*:   (2S,3S)-3-Hydroxy-5-Oxooxolane-2,3-Dicarboxylic Acid
IUPAC Name:   (2S,3S)-3-hydroxy-5-oxooxolane-2,3-dicarboxylic acid
Synonyms:  
Standard InCHIKey:  PFHZIWAVXDSFTB-CVYQJGLWSA-N
Standard InCHI:  InChI=1S/C6H6O7/c7-2-1-6(12,5(10)11)3(13-2)4(8)9/h3,12H,1H2,(H,8,9)(H,10,11)/t3-,6+/m1/s1
SMILES:  O=C1O[C@@H]([C@](C1)(O)C(=O)O)C(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2165253
PubChem CID:   9991606
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0001986] Tricarboxylic 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
NPO6536 Marrubium velutinum Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[17287127]
NPO11266 Garcinia cambogia Species Clusiaceae Eukaryota n.a. exocarp n.a. PMID[21114277]
NPO11266 Garcinia cambogia Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6536 Marrubium velutinum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11266 Garcinia cambogia Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO11266 Garcinia cambogia Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6536 Marrubium velutinum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1330 Stachybotrys alternans Species Stachybotryaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2382 Nicotiana excelsior Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO769 Eria elata Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24463 Linum corymbulosum Species Linaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12849 Lagerstroemia subcostata Species Lythraceae 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
NPT945 Individual Protein ATP-citrate synthase Rattus norvegicus Ki = 50000.0 nM PMID[470316]
NPT945 Individual Protein ATP-citrate synthase Rattus norvegicus Ki = 50000.0 nM PMID[470317]

☑ 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 NPC61567 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
0.875 High Similarity NPC198377
0.8545 High Similarity NPC65985
0.8448 Intermediate Similarity NPC179624
0.8393 Intermediate Similarity NPC6883
0.8246 Intermediate Similarity NPC60830
0.8246 Intermediate Similarity NPC68743
0.8214 Intermediate Similarity NPC19676
0.8214 Intermediate Similarity NPC323401
0.8148 Intermediate Similarity NPC293378
0.7818 Intermediate Similarity NPC46254
0.7667 Intermediate Similarity NPC293692
0.7097 Intermediate Similarity NPC220922
0.7091 Intermediate Similarity NPC38891
0.7091 Intermediate Similarity NPC242655
0.6852 Remote Similarity NPC121018
0.6852 Remote Similarity NPC192402
0.6852 Remote Similarity NPC19044
0.6852 Remote Similarity NPC24751
0.6852 Remote Similarity NPC100742
0.6852 Remote Similarity NPC97444
0.6833 Remote Similarity NPC277878
0.6818 Remote Similarity NPC317651
0.6818 Remote Similarity NPC258690
0.6727 Remote Similarity NPC310220
0.6721 Remote Similarity NPC196612
0.6667 Remote Similarity NPC133771
0.6667 Remote Similarity NPC469925
0.6575 Remote Similarity NPC125164
0.6545 Remote Similarity NPC35661
0.6491 Remote Similarity NPC270088
0.6441 Remote Similarity NPC247546
0.6441 Remote Similarity NPC172086
0.6429 Remote Similarity NPC313565
0.6429 Remote Similarity NPC259982
0.6429 Remote Similarity NPC228782
0.6364 Remote Similarity NPC240109
0.6296 Remote Similarity NPC128713
0.6286 Remote Similarity NPC241949
0.6197 Remote Similarity NPC32148
0.6176 Remote Similarity NPC10659
0.6119 Remote Similarity NPC323945
0.6118 Remote Similarity NPC65359
0.6087 Remote Similarity NPC268243
0.6047 Remote Similarity NPC469627
0.6034 Remote Similarity NPC319680
0.6032 Remote Similarity NPC317680
0.6029 Remote Similarity NPC320296
0.5972 Remote Similarity NPC57788
0.5972 Remote Similarity NPC53879
0.5915 Remote Similarity NPC469926
0.589 Remote Similarity NPC82315
0.5882 Remote Similarity NPC17935
0.5867 Remote Similarity NPC96322
0.5844 Remote Similarity NPC228411
0.5823 Remote Similarity NPC470014
0.5811 Remote Similarity NPC28526
0.5806 Remote Similarity NPC328954
0.5789 Remote Similarity NPC473775
0.5789 Remote Similarity NPC473699
0.5789 Remote Similarity NPC475260
0.5789 Remote Similarity NPC320331
0.5789 Remote Similarity NPC474100
0.5789 Remote Similarity NPC51249
0.5789 Remote Similarity NPC475232
0.5714 Remote Similarity NPC278028
0.5714 Remote Similarity NPC328180
0.5698 Remote Similarity NPC119740
0.5698 Remote Similarity NPC150063
0.5698 Remote Similarity NPC53158
0.5696 Remote Similarity NPC474003
0.5672 Remote Similarity NPC3547
0.5647 Remote Similarity NPC475491
0.5647 Remote Similarity NPC469626
0.5636 Remote Similarity NPC321699
0.5636 Remote Similarity NPC1037
0.5636 Remote Similarity NPC159089
0.5625 Remote Similarity NPC475616
0.5614 Remote Similarity NPC316217
0.5614 Remote Similarity NPC222792

  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 NPC61567 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
0.8302 Intermediate Similarity NPD109 Approved
0.8302 Intermediate Similarity NPD70 Approved
0.8302 Intermediate Similarity NPD9124 Approved
0.8302 Intermediate Similarity NPD108 Approved
0.8302 Intermediate Similarity NPD9123 Approved
0.8302 Intermediate Similarity NPD9125 Approved
0.8302 Intermediate Similarity NPD9128 Approved
0.8302 Intermediate Similarity NPD9122 Approved
0.8302 Intermediate Similarity NPD9127 Approved
0.8302 Intermediate Similarity NPD9121 Approved
0.8302 Intermediate Similarity NPD9130 Phase 3
0.8148 Intermediate Similarity NPD9129 Approved
0.8148 Intermediate Similarity NPD71 Approved
0.8148 Intermediate Similarity NPD9126 Approved
0.7097 Intermediate Similarity NPD8959 Approved
0.6852 Remote Similarity NPD8603 Approved
0.6852 Remote Similarity NPD8604 Approved
0.6852 Remote Similarity NPD8602 Approved
0.6852 Remote Similarity NPD8598 Approved
0.6852 Remote Similarity NPD8600 Approved
0.6852 Remote Similarity NPD8605 Approved
0.6852 Remote Similarity NPD8599 Approved
0.6852 Remote Similarity NPD8601 Approved
0.6833 Remote Similarity NPD9007 Approved
0.6833 Remote Similarity NPD9009 Approved
0.6833 Remote Similarity NPD72 Approved
0.6833 Remote Similarity NPD9010 Approved
0.6833 Remote Similarity NPD65 Approved
0.6833 Remote Similarity NPD66 Approved
0.6833 Remote Similarity NPD64 Approved
0.6833 Remote Similarity NPD9011 Approved
0.6833 Remote Similarity NPD8960 Approved
0.6833 Remote Similarity NPD9008 Approved
0.6818 Remote Similarity NPD8961 Approved
0.6441 Remote Similarity NPD9004 Approved
0.6441 Remote Similarity NPD9003 Clinical (unspecified phase)
0.6441 Remote Similarity NPD9005 Phase 3
0.6406 Remote Similarity NPD73 Approved
0.6197 Remote Similarity NPD896 Approved
0.6197 Remote Similarity NPD897 Approved
0.6197 Remote Similarity NPD898 Approved
0.6129 Remote Similarity NPD9001 Clinical (unspecified phase)
0.6129 Remote Similarity NPD9002 Approved
0.6029 Remote Similarity NPD9120 Clinical (unspecified phase)
0.5641 Remote Similarity NPD1453 Phase 1
0.5641 Remote Similarity NPD376 Approved
0.5641 Remote Similarity NPD11 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