Structure

Physi-Chem Properties

Molecular Weight:  234.07
Volume:  217.843
LogP:  0.076
LogD:  0.193
LogS:  -0.555
# Rotatable Bonds:  8
TPSA:  99.13
# H-Bond Aceptor:  7
# H-Bond Donor:  1
# Rings:  0
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.482
Synthetic Accessibility Score:  2.537
Fsp3:  0.667
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.833
MDCK Permeability:  0.00041670360951684415
Pgp-inhibitor:  0.015
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.478
20% Bioavailability (F20%):  0.419
30% Bioavailability (F30%):  0.995

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.702
Plasma Protein Binding (PPB):  17.37683868408203%
Volume Distribution (VD):  0.348
Pgp-substrate:  65.8640365600586%

ADMET: Metabolism

CYP1A2-inhibitor:  0.015
CYP1A2-substrate:  0.253
CYP2C19-inhibitor:  0.05
CYP2C19-substrate:  0.437
CYP2C9-inhibitor:  0.005
CYP2C9-substrate:  0.182
CYP2D6-inhibitor:  0.007
CYP2D6-substrate:  0.167
CYP3A4-inhibitor:  0.007
CYP3A4-substrate:  0.207

ADMET: Excretion

Clearance (CL):  5.093
Half-life (T1/2):  0.871

ADMET: Toxicity

hERG Blockers:  0.01
Human Hepatotoxicity (H-HT):  0.53
Drug-inuced Liver Injury (DILI):  0.589
AMES Toxicity:  0.031
Rat Oral Acute Toxicity:  0.003
Maximum Recommended Daily Dose:  0.062
Skin Sensitization:  0.044
Carcinogencity:  0.019
Eye Corrosion:  0.75
Eye Irritation:  0.505
Respiratory Toxicity:  0.019

Download Data

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

  Natural Product: NPC68743

Natural Product ID:  NPC68743
Common Name*:   Trimethyl 2-Hydroxypropane-1,2,3-Tricarboxylate
IUPAC Name:   trimethyl 2-hydroxypropane-1,2,3-tricarboxylate
Synonyms:  
Standard InCHIKey:  HDDLVZWGOPWKFW-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C9H14O7/c1-14-6(10)4-9(13,8(12)16-3)5-7(11)15-2/h13H,4-5H2,1-3H3
SMILES:  COC(=O)C(CC(=O)OC)(CC(=O)OC)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL455514
PubChem CID:   74112
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
NPO28679 Prunus mume Species Rosaceae Eukaryota flowers n.a. n.a. PMID[12193020]
NPO7863 Dioscorea opposita Species Dioscoreaceae Eukaryota aerial parts n.a. n.a. PMID[16124773]
NPO12631 Corylus avellana Species Betulaceae Eukaryota Shells; Leaves n.a. n.a. PMID[18163585]
NPO1103 Dioscorea japonica Species Dioscoreaceae Eukaryota rhizomes n.a. n.a. PMID[21353549]
NPO28679 Prunus mume Species Rosaceae Eukaryota fruits n.a. n.a. PMID[24485782]
NPO24833 Dioscorea polystachya Species Dioscoreaceae Eukaryota n.a. bark n.a. PMID[24689699]
NPO12631 Corylus avellana Species Betulaceae Eukaryota n.a. n.a. n.a. PMID[25420236]
NPO12631 Corylus avellana Species Betulaceae Eukaryota Leaves n.a. n.a. PMID[26606246]
NPO12631 Corylus avellana Species Betulaceae Eukaryota Green Leafy Covers n.a. n.a. PMID[28520428]
NPO12631 Corylus avellana Species Betulaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO12631 Corylus avellana Species Betulaceae Eukaryota n.a. n.a. Database[FooDB]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1103 Dioscorea japonica Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24833 Dioscorea polystachya Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO1103 Dioscorea japonica Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO7863 Dioscorea opposita Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO24833 Dioscorea polystachya Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO7863 Dioscorea opposita Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO1103 Dioscorea japonica Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO28679 Prunus mume Species Rosaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO24833 Dioscorea polystachya Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1103 Dioscorea japonica Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7863 Dioscorea opposita Species Dioscoreaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12631 Corylus avellana Species Betulaceae 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
NPT32 Organism Mus musculus Mus musculus Activity = 29.0 % PMID[465636]
NPT19 Organism Escherichia coli Escherichia coli IZ = 11.33 mm PMID[465637]
NPT314 Organism Bacillus cereus Bacillus cereus IZ = 0.0 mm PMID[465637]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa IZ = 6.67 mm PMID[465637]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus IZ = 11.33 mm PMID[465637]

☑ 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 NPC68743 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 NPC60830
0.9608 High Similarity NPC65985
0.9444 High Similarity NPC179624
0.9434 High Similarity NPC198377
0.8824 High Similarity NPC293378
0.8364 Intermediate Similarity NPC6883
0.8246 Intermediate Similarity NPC61567
0.8182 Intermediate Similarity NPC323401
0.8182 Intermediate Similarity NPC19676
0.7647 Intermediate Similarity NPC310220
0.7231 Intermediate Similarity NPC241949
0.7037 Intermediate Similarity NPC242655
0.7037 Intermediate Similarity NPC38891
0.6923 Remote Similarity NPC240109
0.6909 Remote Similarity NPC133771
0.6842 Remote Similarity NPC46254
0.678 Remote Similarity NPC277878
0.6774 Remote Similarity NPC220922
0.6774 Remote Similarity NPC293692
0.6667 Remote Similarity NPC206924
0.6667 Remote Similarity NPC196612
0.6538 Remote Similarity NPC128713
0.65 Remote Similarity NPC317680
0.6481 Remote Similarity NPC192402
0.6481 Remote Similarity NPC100742
0.6481 Remote Similarity NPC121018
0.6481 Remote Similarity NPC24751
0.6481 Remote Similarity NPC97444
0.6481 Remote Similarity NPC35661
0.6481 Remote Similarity NPC19044
0.6429 Remote Similarity NPC270088
0.6379 Remote Similarity NPC247546
0.6379 Remote Similarity NPC172086
0.6377 Remote Similarity NPC32148
0.6377 Remote Similarity NPC469925
0.6364 Remote Similarity NPC313565
0.6364 Remote Similarity NPC259982
0.6364 Remote Similarity NPC469923
0.6364 Remote Similarity NPC228782
0.6301 Remote Similarity NPC125164
0.6269 Remote Similarity NPC317651
0.6269 Remote Similarity NPC258690
0.625 Remote Similarity NPC319680
0.6226 Remote Similarity NPC325454
0.6061 Remote Similarity NPC323945
0.6053 Remote Similarity NPC474003
0.6038 Remote Similarity NPC317945
0.6027 Remote Similarity NPC96322
0.6 Remote Similarity NPC320331
0.597 Remote Similarity NPC320296
0.5926 Remote Similarity NPC38930
0.5915 Remote Similarity NPC286842
0.5915 Remote Similarity NPC57788
0.5915 Remote Similarity NPC53879
0.5909 Remote Similarity NPC320032
0.5882 Remote Similarity NPC125575
0.5882 Remote Similarity NPC65359
0.5849 Remote Similarity NPC1037
0.5846 Remote Similarity NPC473936
0.5821 Remote Similarity NPC475821
0.5821 Remote Similarity NPC17935
0.5818 Remote Similarity NPC222792
0.5818 Remote Similarity NPC316217
0.5814 Remote Similarity NPC469627
0.5797 Remote Similarity NPC268243
0.5789 Remote Similarity NPC228411
0.5769 Remote Similarity NPC127142
0.5769 Remote Similarity NPC470014
0.5769 Remote Similarity NPC7814
0.5738 Remote Similarity NPC328954
0.5735 Remote Similarity NPC469921
0.5686 Remote Similarity NPC212144
0.5672 Remote Similarity NPC322855
0.5667 Remote Similarity NPC278028
0.5667 Remote Similarity NPC328180
0.5652 Remote Similarity NPC469922
0.5652 Remote Similarity NPC10659
0.5641 Remote Similarity NPC108014
0.5634 Remote Similarity NPC469926
0.5634 Remote Similarity NPC476330
0.5616 Remote Similarity NPC82315
0.5606 Remote Similarity NPC3547

  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 NPC68743 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
0.8824 High Similarity NPD71 Approved
0.8824 High Similarity NPD9126 Approved
0.8824 High Similarity NPD9129 Approved
0.8627 High Similarity NPD70 Approved
0.8627 High Similarity NPD9122 Approved
0.8627 High Similarity NPD9127 Approved
0.8627 High Similarity NPD9130 Phase 3
0.8627 High Similarity NPD109 Approved
0.8627 High Similarity NPD9128 Approved
0.8627 High Similarity NPD9121 Approved
0.8627 High Similarity NPD9124 Approved
0.8627 High Similarity NPD108 Approved
0.8627 High Similarity NPD9123 Approved
0.8627 High Similarity NPD9125 Approved
0.678 Remote Similarity NPD9007 Approved
0.678 Remote Similarity NPD9009 Approved
0.678 Remote Similarity NPD65 Approved
0.678 Remote Similarity NPD8960 Approved
0.678 Remote Similarity NPD9008 Approved
0.678 Remote Similarity NPD9010 Approved
0.678 Remote Similarity NPD64 Approved
0.678 Remote Similarity NPD66 Approved
0.678 Remote Similarity NPD72 Approved
0.678 Remote Similarity NPD9011 Approved
0.6774 Remote Similarity NPD8959 Approved
0.6481 Remote Similarity NPD8605 Approved
0.6481 Remote Similarity NPD8603 Approved
0.6481 Remote Similarity NPD8602 Approved
0.6481 Remote Similarity NPD8604 Approved
0.6481 Remote Similarity NPD8600 Approved
0.6481 Remote Similarity NPD8601 Approved
0.6481 Remote Similarity NPD8598 Approved
0.6481 Remote Similarity NPD8599 Approved
0.6379 Remote Similarity NPD9003 Clinical (unspecified phase)
0.6379 Remote Similarity NPD9004 Approved
0.6379 Remote Similarity NPD9005 Phase 3
0.6377 Remote Similarity NPD897 Approved
0.6377 Remote Similarity NPD896 Approved
0.6377 Remote Similarity NPD898 Approved
0.6349 Remote Similarity NPD73 Approved
0.6269 Remote Similarity NPD8961 Approved
0.6066 Remote Similarity NPD9002 Approved
0.6066 Remote Similarity NPD9001 Clinical (unspecified phase)
0.6 Remote Similarity NPD376 Approved
0.6 Remote Similarity NPD11 Approved
0.5769 Remote Similarity NPD8857 Approved
0.5696 Remote Similarity NPD7329 Approved
0.5614 Remote Similarity NPD9116 Phase 1

  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