Structure

Physi-Chem Properties

Molecular Weight:  208.02
Volume:  174.745
LogP:  -1.642
LogD:  -1.224
LogS:  -0.68
# Rotatable Bonds:  5
TPSA:  152.36
# H-Bond Aceptor:  8
# H-Bond Donor:  5
# Rings:  0
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.239
Synthetic Accessibility Score:  3.564
Fsp3:  0.5
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.228
MDCK Permeability:  0.004881733562797308
Pgp-inhibitor:  0.0
Pgp-substrate:  0.974
Human Intestinal Absorption (HIA):  0.076
20% Bioavailability (F20%):  0.003
30% Bioavailability (F30%):  0.384

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.347
Plasma Protein Binding (PPB):  16.573856353759766%
Volume Distribution (VD):  0.324
Pgp-substrate:  72.03135681152344%

ADMET: Metabolism

CYP1A2-inhibitor:  0.001
CYP1A2-substrate:  0.044
CYP2C19-inhibitor:  0.021
CYP2C19-substrate:  0.041
CYP2C9-inhibitor:  0.005
CYP2C9-substrate:  0.472
CYP2D6-inhibitor:  0.003
CYP2D6-substrate:  0.076
CYP3A4-inhibitor:  0.016
CYP3A4-substrate:  0.002

ADMET: Excretion

Clearance (CL):  1.587
Half-life (T1/2):  0.811

ADMET: Toxicity

hERG Blockers:  0.002
Human Hepatotoxicity (H-HT):  0.191
Drug-inuced Liver Injury (DILI):  0.892
AMES Toxicity:  0.041
Rat Oral Acute Toxicity:  0.012
Maximum Recommended Daily Dose:  0.025
Skin Sensitization:  0.645
Carcinogencity:  0.031
Eye Corrosion:  0.934
Eye Irritation:  0.986
Respiratory Toxicity:  0.57

Download Data

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

  Natural Product: NPC6883

Natural Product ID:  NPC6883
Common Name*:   (-)-Hydroxycitrate
IUPAC Name:   (1S,2S)-1,2-dihydroxypropane-1,2,3-tricarboxylic acid
Synonyms:   (-)-Hydroxycitrate
Standard InCHIKey:  ZMJBYMUCKBYSCP-CVYQJGLWSA-N
Standard InCHI:  InChI=1S/C6H8O8/c7-2(8)1-6(14,5(12)13)3(9)4(10)11/h3,9,14H,1H2,(H,7,8)(H,10,11)(H,12,13)/t3-,6+/m1/s1
SMILES:  OC(=O)C[C@]([C@@H](C(=O)O)O)(C(=O)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL118715
PubChem CID:   185620
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]
NPO6536 Marrubium velutinum Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12849 Lagerstroemia subcostata Species Lythraceae 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]

☑ 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
NPT65 Cell Line HepG2 Homo sapiens Control = 87.0 % PMID[571520]
NPT65 Cell Line HepG2 Homo sapiens Control = 100.0 % PMID[571520]
NPT65 Cell Line HepG2 Homo sapiens Control = 40.0 % PMID[571520]
NPT65 Cell Line HepG2 Homo sapiens Control = 79.0 % PMID[571520]
NPT65 Cell Line HepG2 Homo sapiens Control = 103.0 % PMID[571520]
NPT65 Cell Line HepG2 Homo sapiens Control = 15.0 % PMID[571520]
NPT65 Cell Line HepG2 Homo sapiens Control = 57.0 % PMID[571520]
NPT65 Cell Line HepG2 Homo sapiens Control = 104.0 % PMID[571520]
NPT65 Cell Line HepG2 Homo sapiens Control = 110.0 % PMID[571522]
NPT65 Cell Line HepG2 Homo sapiens Control = 40.0 % PMID[571522]
NPT65 Cell Line HepG2 Homo sapiens Control = 15.0 % PMID[571522]
NPT65 Cell Line HepG2 Homo sapiens Control = 87.0 % PMID[571522]
NPT65 Cell Line HepG2 Homo sapiens Control = 79.0 % PMID[571522]
NPT65 Cell Line HepG2 Homo sapiens Control = 57.0 % PMID[571522]
NPT65 Cell Line HepG2 Homo sapiens Control = 100.0 % PMID[571522]
NPT65 Cell Line HepG2 Homo sapiens Control = 103.0 % PMID[571522]
NPT65 Cell Line HepG2 Homo sapiens Control = 104.0 % PMID[571522]
NPT945 Individual Protein ATP-citrate synthase Rattus norvegicus Ki = 150.0 nM PMID[571521]
NPT946 Individual Protein ATP-citrate synthase Homo sapiens IC50 = 150.0 nM PMID[571523]
NPT945 Individual Protein ATP-citrate synthase Rattus norvegicus Ki = 8000.0 nM PMID[571524]
NPT945 Individual Protein ATP-citrate synthase Rattus norvegicus Ki = 150.0 nM PMID[571524]
NPT946 Individual Protein ATP-citrate synthase Homo sapiens Ki = 300000.0 nM PMID[571526]
NPT945 Individual Protein ATP-citrate synthase Rattus norvegicus Ki = 8000.0 nM PMID[571526]

☑ 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 NPC6883 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
0.9412 High Similarity NPC323401
0.9412 High Similarity NPC19676
0.9 High Similarity NPC293378
0.8679 High Similarity NPC65985
0.8545 High Similarity NPC198377
0.8393 Intermediate Similarity NPC61567
0.8364 Intermediate Similarity NPC68743
0.8364 Intermediate Similarity NPC60830
0.8246 Intermediate Similarity NPC179624
0.82 Intermediate Similarity NPC242655
0.82 Intermediate Similarity NPC38891
0.8 Intermediate Similarity NPC196612
0.7818 Intermediate Similarity NPC277878
0.76 Intermediate Similarity NPC100742
0.76 Intermediate Similarity NPC121018
0.76 Intermediate Similarity NPC24751
0.76 Intermediate Similarity NPC192402
0.76 Intermediate Similarity NPC35661
0.76 Intermediate Similarity NPC97444
0.76 Intermediate Similarity NPC19044
0.75 Intermediate Similarity NPC270088
0.7451 Intermediate Similarity NPC310220
0.7451 Intermediate Similarity NPC228782
0.7451 Intermediate Similarity NPC259982
0.7451 Intermediate Similarity NPC313565
0.7407 Intermediate Similarity NPC172086
0.7407 Intermediate Similarity NPC247546
0.7273 Intermediate Similarity NPC46254
0.7213 Intermediate Similarity NPC323945
0.7167 Intermediate Similarity NPC293692
0.7167 Intermediate Similarity NPC220922
0.7097 Intermediate Similarity NPC320296
0.7059 Intermediate Similarity NPC240109
0.6981 Remote Similarity NPC319680
0.6964 Remote Similarity NPC328954
0.6897 Remote Similarity NPC317680
0.6818 Remote Similarity NPC241949
0.6731 Remote Similarity NPC320331
0.6727 Remote Similarity NPC133771
0.6721 Remote Similarity NPC3547
0.6716 Remote Similarity NPC53879
0.6716 Remote Similarity NPC57788
0.6667 Remote Similarity NPC128713
0.6615 Remote Similarity NPC317651
0.6615 Remote Similarity NPC258690
0.6538 Remote Similarity NPC316217
0.6538 Remote Similarity NPC222792
0.6471 Remote Similarity NPC32148
0.6275 Remote Similarity NPC159089
0.6275 Remote Similarity NPC5505
0.6232 Remote Similarity NPC469925
0.6164 Remote Similarity NPC125164
0.6119 Remote Similarity NPC88898
0.6119 Remote Similarity NPC106216
0.6078 Remote Similarity NPC168052
0.6078 Remote Similarity NPC250870
0.6078 Remote Similarity NPC191084
0.6038 Remote Similarity NPC325454
0.6 Remote Similarity NPC125575
0.5962 Remote Similarity NPC1037
0.5921 Remote Similarity NPC474003
0.5909 Remote Similarity NPC475821
0.5909 Remote Similarity NPC17935
0.5882 Remote Similarity NPC268243
0.5849 Remote Similarity NPC317945
0.5849 Remote Similarity NPC206924
0.5846 Remote Similarity NPC43169
0.5846 Remote Similarity NPC112224
0.5846 Remote Similarity NPC93861
0.5846 Remote Similarity NPC327895
0.58 Remote Similarity NPC149070
0.58 Remote Similarity NPC197207
0.58 Remote Similarity NPC127074
0.58 Remote Similarity NPC182541
0.58 Remote Similarity NPC187058
0.5789 Remote Similarity NPC320624
0.5789 Remote Similarity NPC318951
0.5769 Remote Similarity NPC316685
0.5765 Remote Similarity NPC65359
0.5741 Remote Similarity NPC38930
0.5733 Remote Similarity NPC317212
0.5714 Remote Similarity NPC325307
0.5714 Remote Similarity NPC322956
0.5714 Remote Similarity NPC476330
0.5667 Remote Similarity NPC131770
0.5667 Remote Similarity NPC200618
0.5652 Remote Similarity NPC474552
0.5616 Remote Similarity NPC28526
0.56 Remote Similarity NPC198126

  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 NPC6883 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
0.9 High Similarity NPD9129 Approved
0.9 High Similarity NPD71 Approved
0.9 High Similarity NPD9126 Approved
0.88 High Similarity NPD9125 Approved
0.88 High Similarity NPD9130 Phase 3
0.88 High Similarity NPD70 Approved
0.88 High Similarity NPD9122 Approved
0.88 High Similarity NPD9121 Approved
0.88 High Similarity NPD9127 Approved
0.88 High Similarity NPD9128 Approved
0.88 High Similarity NPD9123 Approved
0.88 High Similarity NPD109 Approved
0.88 High Similarity NPD9124 Approved
0.88 High Similarity NPD108 Approved
0.7818 Intermediate Similarity NPD9010 Approved
0.7818 Intermediate Similarity NPD66 Approved
0.7818 Intermediate Similarity NPD72 Approved
0.7818 Intermediate Similarity NPD64 Approved
0.7818 Intermediate Similarity NPD8960 Approved
0.7818 Intermediate Similarity NPD9007 Approved
0.7818 Intermediate Similarity NPD9011 Approved
0.7818 Intermediate Similarity NPD65 Approved
0.7818 Intermediate Similarity NPD9008 Approved
0.7818 Intermediate Similarity NPD9009 Approved
0.76 Intermediate Similarity NPD8604 Approved
0.76 Intermediate Similarity NPD8605 Approved
0.76 Intermediate Similarity NPD8601 Approved
0.76 Intermediate Similarity NPD8600 Approved
0.76 Intermediate Similarity NPD8602 Approved
0.76 Intermediate Similarity NPD8599 Approved
0.76 Intermediate Similarity NPD8598 Approved
0.76 Intermediate Similarity NPD8603 Approved
0.7586 Intermediate Similarity NPD73 Approved
0.7407 Intermediate Similarity NPD9004 Approved
0.7407 Intermediate Similarity NPD9003 Clinical (unspecified phase)
0.7407 Intermediate Similarity NPD9005 Phase 3
0.7167 Intermediate Similarity NPD8959 Approved
0.7018 Intermediate Similarity NPD9002 Approved
0.7018 Intermediate Similarity NPD9001 Clinical (unspecified phase)
0.6615 Remote Similarity NPD8961 Approved
0.6471 Remote Similarity NPD898 Approved
0.6471 Remote Similarity NPD896 Approved
0.6471 Remote Similarity NPD897 Approved
0.6379 Remote Similarity NPD8964 Approved
0.6029 Remote Similarity NPD7909 Approved
0.5867 Remote Similarity NPD376 Approved
0.5867 Remote Similarity NPD11 Approved
0.5821 Remote Similarity NPD9120 Clinical (unspecified phase)
0.58 Remote Similarity NPD8814 Phase 3
0.5714 Remote Similarity NPD9116 Phase 1
0.56 Remote Similarity NPD8618 Approved
0.56 Remote Similarity NPD3181 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