Structure

Physi-Chem Properties

Molecular Weight:  192.03
Volume:  165.955
LogP:  -1.811
LogD:  -0.764
LogS:  -0.132
# Rotatable Bonds:  5
TPSA:  132.13
# H-Bond Aceptor:  7
# H-Bond Donor:  4
# Rings:  0
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.226
Synthetic Accessibility Score:  3.356
Fsp3:  0.5
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:  -6.282
MDCK Permeability:  0.005751531571149826
Pgp-inhibitor:  0.0
Pgp-substrate:  0.351
Human Intestinal Absorption (HIA):  0.969
20% Bioavailability (F20%):  0.991
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.385
Plasma Protein Binding (PPB):  24.279010772705078%
Volume Distribution (VD):  0.267
Pgp-substrate:  49.403900146484375%

ADMET: Metabolism

CYP1A2-inhibitor:  0.003
CYP1A2-substrate:  0.027
CYP2C19-inhibitor:  0.026
CYP2C19-substrate:  0.038
CYP2C9-inhibitor:  0.01
CYP2C9-substrate:  0.594
CYP2D6-inhibitor:  0.012
CYP2D6-substrate:  0.106
CYP3A4-inhibitor:  0.012
CYP3A4-substrate:  0.005

ADMET: Excretion

Clearance (CL):  2.269
Half-life (T1/2):  0.899

ADMET: Toxicity

hERG Blockers:  0.009
Human Hepatotoxicity (H-HT):  0.177
Drug-inuced Liver Injury (DILI):  0.376
AMES Toxicity:  0.021
Rat Oral Acute Toxicity:  0.004
Maximum Recommended Daily Dose:  0.006
Skin Sensitization:  0.296
Carcinogencity:  0.012
Eye Corrosion:  0.079
Eye Irritation:  0.831
Respiratory Toxicity:  0.196

Download Data

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

  Natural Product: NPC19676

Natural Product ID:  NPC19676
Common Name*:   L-Isocitrate
IUPAC Name:   (1S,2R)-1-hydroxypropane-1,2,3-tricarboxylic acid
Synonyms:   L-Isocitrate
Standard InCHIKey:  ODBLHEXUDAPZAU-FONMRSAGSA-N
Standard InCHI:  InChI=1S/C6H8O7/c7-3(8)1-2(5(10)11)4(9)6(12)13/h2,4,9H,1H2,(H,7,8)(H,10,11)(H,12,13)/t2-,4+/m1/s1
SMILES:  C([C@H]([C@@H](C(=O)O)O)C(=O)O)C(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2338331
PubChem CID:   440409
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
NPO210 Uvaria calamistrata Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[10075755]
NPO210 Uvaria calamistrata Species Annonaceae Eukaryota n.a. n.a. n.a. PMID[11000019]
NPO11248 Tachigalia paniculata n.a. n.a. n.a. leaves n.a. n.a. PMID[12444671]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. leaf n.a. PMID[18409045]
NPO29141 Panax ginseng Species Araliaceae Eukaryota flower buds n.a. n.a. PMID[19926279]
NPO10540 Passiflora incarnata Species Passifloraceae Eukaryota n.a. n.a. n.a. PMID[2026709]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. root n.a. PMID[2092947]
NPO29141 Panax ginseng Species Araliaceae Eukaryota berry n.a. n.a. PMID[21216145]
NPO29141 Panax ginseng Species Araliaceae Eukaryota leaves n.a. n.a. PMID[24290061]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[24968750]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[25152999]
NPO29141 Panax ginseng Species Araliaceae Eukaryota stems-leaves n.a. n.a. PMID[26420067]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. stem n.a. PMID[27914541]
NPO29141 Panax ginseng Species Araliaceae Eukaryota Flower Buds n.a. n.a. PMID[28345906]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. PMID[32129622]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO10540 Passiflora incarnata Species Passifloraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[MetaboLights]
NPO10540 Passiflora incarnata Species Passifloraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO13166 Nicotiana undulata Species Solanaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO731 Panax schinseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11248 Tachigalia paniculata n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO11488 Alstonia muelleriana Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14354 Artemisia cina Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5189 Glycine tomentella Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO12001 Saccharomyces pastori Species Saccharomycetaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10540 Passiflora incarnata Species Passifloraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21854 Pterocladiella tenuis Species Gelidiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18805 Tripolium pannonicum Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11642 Dacrydium cupressinum Species Podocarpaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO210 Uvaria calamistrata Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14255 Streptomyces flocculus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO12684 Trigonella grandiflora Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO29141 Panax ginseng Species Araliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19635 Coreopsis nodosa Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13568 Hypoxylon rubiginosum Species Xylariaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7998 Senecio paludaffinis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22666 Haematococcus lacustris Species Haematococcaceae 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
NPT1510 Individual Protein Alpha-ketoglutarate-dependent dioxygenase FTO Homo sapiens IC50 > 1000000.0 nM PMID[557195]

☑ 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 NPC19676 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 NPC323401
0.9412 High Similarity NPC6883
0.88 High Similarity NPC293378
0.8491 Intermediate Similarity NPC65985
0.8367 Intermediate Similarity NPC38891
0.8367 Intermediate Similarity NPC242655
0.8364 Intermediate Similarity NPC198377
0.8214 Intermediate Similarity NPC61567
0.8182 Intermediate Similarity NPC68743
0.8182 Intermediate Similarity NPC60830
0.807 Intermediate Similarity NPC179624
0.7963 Intermediate Similarity NPC277878
0.7818 Intermediate Similarity NPC196612
0.7755 Intermediate Similarity NPC192402
0.7755 Intermediate Similarity NPC19044
0.7755 Intermediate Similarity NPC97444
0.7755 Intermediate Similarity NPC24751
0.7755 Intermediate Similarity NPC121018
0.7755 Intermediate Similarity NPC100742
0.7755 Intermediate Similarity NPC35661
0.7647 Intermediate Similarity NPC270088
0.76 Intermediate Similarity NPC313565
0.76 Intermediate Similarity NPC259982
0.76 Intermediate Similarity NPC228782
0.7551 Intermediate Similarity NPC240109
0.7547 Intermediate Similarity NPC172086
0.7547 Intermediate Similarity NPC247546
0.7451 Intermediate Similarity NPC319680
0.7407 Intermediate Similarity NPC46254
0.7288 Intermediate Similarity NPC293692
0.7288 Intermediate Similarity NPC220922
0.7255 Intermediate Similarity NPC310220
0.7049 Intermediate Similarity NPC323945
0.7 Intermediate Similarity NPC222792
0.7 Intermediate Similarity NPC316217
0.6935 Remote Similarity NPC320296
0.6923 Remote Similarity NPC241949
0.6863 Remote Similarity NPC320331
0.68 Remote Similarity NPC128713
0.6786 Remote Similarity NPC328954
0.6719 Remote Similarity NPC258690
0.6719 Remote Similarity NPC317651
0.6567 Remote Similarity NPC53879
0.6567 Remote Similarity NPC57788
0.6557 Remote Similarity NPC3547
0.6545 Remote Similarity NPC133771
0.6471 Remote Similarity NPC325454
0.6441 Remote Similarity NPC317680
0.64 Remote Similarity NPC159089
0.64 Remote Similarity NPC5505
0.6324 Remote Similarity NPC32148
0.6212 Remote Similarity NPC106216
0.6212 Remote Similarity NPC88898
0.62 Remote Similarity NPC250870
0.62 Remote Similarity NPC168052
0.62 Remote Similarity NPC191084
0.62 Remote Similarity NPC316685
0.6154 Remote Similarity NPC38930
0.6122 Remote Similarity NPC125575
0.6087 Remote Similarity NPC469925
0.6078 Remote Similarity NPC1037
0.6027 Remote Similarity NPC317212
0.6027 Remote Similarity NPC125164
0.6 Remote Similarity NPC17935
0.6 Remote Similarity NPC475821
0.5962 Remote Similarity NPC317945
0.5962 Remote Similarity NPC206924
0.5938 Remote Similarity NPC43169
0.5938 Remote Similarity NPC327895
0.5938 Remote Similarity NPC93861
0.5938 Remote Similarity NPC112224
0.5918 Remote Similarity NPC149070
0.5918 Remote Similarity NPC127074
0.5918 Remote Similarity NPC187058
0.5918 Remote Similarity NPC182541
0.5918 Remote Similarity NPC197207
0.5915 Remote Similarity NPC28526
0.5818 Remote Similarity NPC322956
0.5818 Remote Similarity NPC325307
0.5797 Remote Similarity NPC476330
0.5789 Remote Similarity NPC474003
0.5775 Remote Similarity NPC82315
0.5763 Remote Similarity NPC131770
0.5763 Remote Similarity NPC200618
0.5758 Remote Similarity NPC470363
0.5735 Remote Similarity NPC474552
0.5735 Remote Similarity NPC268243
0.5733 Remote Similarity NPC228411
0.5714 Remote Similarity NPC198126
0.5692 Remote Similarity NPC190385
0.5686 Remote Similarity NPC127142
0.5686 Remote Similarity NPC7814
0.5686 Remote Similarity NPC307027
0.5676 Remote Similarity NPC51249
0.5676 Remote Similarity NPC473699
0.5676 Remote Similarity NPC474100
0.5676 Remote Similarity NPC475260
0.5676 Remote Similarity NPC473775
0.5676 Remote Similarity NPC475232
0.5647 Remote Similarity NPC65359
0.5614 Remote Similarity NPC320624
0.5614 Remote Similarity NPC318951
0.5606 Remote Similarity NPC320032
0.56 Remote Similarity NPC76217
0.56 Remote Similarity NPC307739
0.56 Remote Similarity NPC280532

  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 NPC19676 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
0.88 High Similarity NPD9129 Approved
0.88 High Similarity NPD9126 Approved
0.88 High Similarity NPD71 Approved
0.86 High Similarity NPD9130 Phase 3
0.86 High Similarity NPD9125 Approved
0.86 High Similarity NPD9122 Approved
0.86 High Similarity NPD9121 Approved
0.86 High Similarity NPD9128 Approved
0.86 High Similarity NPD9123 Approved
0.86 High Similarity NPD70 Approved
0.86 High Similarity NPD9127 Approved
0.86 High Similarity NPD109 Approved
0.86 High Similarity NPD108 Approved
0.86 High Similarity NPD9124 Approved
0.7963 Intermediate Similarity NPD65 Approved
0.7963 Intermediate Similarity NPD9007 Approved
0.7963 Intermediate Similarity NPD9009 Approved
0.7963 Intermediate Similarity NPD64 Approved
0.7963 Intermediate Similarity NPD72 Approved
0.7963 Intermediate Similarity NPD9010 Approved
0.7963 Intermediate Similarity NPD9011 Approved
0.7963 Intermediate Similarity NPD66 Approved
0.7963 Intermediate Similarity NPD9008 Approved
0.7963 Intermediate Similarity NPD8960 Approved
0.7755 Intermediate Similarity NPD8598 Approved
0.7755 Intermediate Similarity NPD8599 Approved
0.7755 Intermediate Similarity NPD8601 Approved
0.7755 Intermediate Similarity NPD8602 Approved
0.7755 Intermediate Similarity NPD8604 Approved
0.7755 Intermediate Similarity NPD8605 Approved
0.7755 Intermediate Similarity NPD8603 Approved
0.7755 Intermediate Similarity NPD8600 Approved
0.7547 Intermediate Similarity NPD9003 Clinical (unspecified phase)
0.7547 Intermediate Similarity NPD9004 Approved
0.7547 Intermediate Similarity NPD9005 Phase 3
0.7414 Intermediate Similarity NPD73 Approved
0.7288 Intermediate Similarity NPD8959 Approved
0.7143 Intermediate Similarity NPD9001 Clinical (unspecified phase)
0.7143 Intermediate Similarity NPD9002 Approved
0.6719 Remote Similarity NPD8961 Approved
0.6491 Remote Similarity NPD8964 Approved
0.6324 Remote Similarity NPD898 Approved
0.6324 Remote Similarity NPD896 Approved
0.6324 Remote Similarity NPD897 Approved
0.6119 Remote Similarity NPD7909 Approved
0.5918 Remote Similarity NPD8814 Phase 3
0.5909 Remote Similarity NPD9120 Clinical (unspecified phase)
0.5893 Remote Similarity NPD8975 Clinical (unspecified phase)
0.5818 Remote Similarity NPD9116 Phase 1
0.5789 Remote Similarity NPD8974 Clinical (unspecified phase)
0.5733 Remote Similarity NPD11 Approved
0.5733 Remote Similarity NPD376 Approved
0.5714 Remote Similarity NPD8618 Approved
0.5692 Remote Similarity NPD9023 Clinical (unspecified phase)
0.5686 Remote Similarity NPD8857 Approved
0.56 Remote Similarity NPD8205 Approved
0.56 Remote Similarity NPD8202 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