Structure

Physi-Chem Properties

Molecular Weight:  112.02
Volume:  104.941
LogP:  0.661
LogD:  0.953
LogS:  -0.116
# Rotatable Bonds:  0
TPSA:  43.37
# H-Bond Aceptor:  3
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.327
Synthetic Accessibility Score:  3.052
Fsp3:  0.2
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.349
MDCK Permeability:  4.141739191254601e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.981
30% Bioavailability (F30%):  0.826

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.928
Plasma Protein Binding (PPB):  43.309295654296875%
Volume Distribution (VD):  0.321
Pgp-substrate:  57.12937545776367%

ADMET: Metabolism

CYP1A2-inhibitor:  0.735
CYP1A2-substrate:  0.251
CYP2C19-inhibitor:  0.448
CYP2C19-substrate:  0.387
CYP2C9-inhibitor:  0.305
CYP2C9-substrate:  0.653
CYP2D6-inhibitor:  0.016
CYP2D6-substrate:  0.207
CYP3A4-inhibitor:  0.037
CYP3A4-substrate:  0.191

ADMET: Excretion

Clearance (CL):  7.435
Half-life (T1/2):  0.917

ADMET: Toxicity

hERG Blockers:  0.002
Human Hepatotoxicity (H-HT):  0.017
Drug-inuced Liver Injury (DILI):  0.025
AMES Toxicity:  0.061
Rat Oral Acute Toxicity:  0.938
Maximum Recommended Daily Dose:  0.441
Skin Sensitization:  0.959
Carcinogencity:  0.16
Eye Corrosion:  0.994
Eye Irritation:  0.99
Respiratory Toxicity:  0.864

Download Data

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

  Natural Product: NPC190649

Natural Product ID:  NPC190649
Common Name*:   Itaconic Anhydride
IUPAC Name:   3-methylideneoxolane-2,5-dione
Synonyms:   Itaconic Anhydride
Standard InCHIKey:  OFNISBHGPNMTMS-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C5H4O3/c1-3-2-4(6)8-5(3)7/h1-2H2
SMILES:  O=C1OC(=O)C(=C)C1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL87967
PubChem CID:   75110
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0000346] Dicarboxylic 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
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. PMID[16562834]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. fruit n.a. PMID[24155209]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. PMID[24959987]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. PMID[25302569]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8187 Schisandra chinensis Species Schisandraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8187 Schisandra chinensis Species Schisandraceae 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
NPT116 Cell Line HL-60 Homo sapiens IC50 > 50000.0 nM PMID[529380]
NPT1180 Protein Complex Protein farnesyltransferase Homo sapiens IC50 > 1000000.0 nM PMID[529379]
NPT1181 Protein Complex Geranylgeranyl transferase type I Homo sapiens IC50 > 1000000.0 nM PMID[529379]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 > 50000.0 nM PMID[529380]

☑ 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 NPC190649 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
0.9268 High Similarity NPC40805
0.7333 Intermediate Similarity NPC169098
0.6471 Remote Similarity NPC137419
0.6471 Remote Similarity NPC122212
0.6441 Remote Similarity NPC474658
0.641 Remote Similarity NPC283626
0.6383 Remote Similarity NPC159773
0.6364 Remote Similarity NPC9290
0.6346 Remote Similarity NPC15789
0.6327 Remote Similarity NPC312547
0.6154 Remote Similarity NPC135698
0.6071 Remote Similarity NPC173157
0.6038 Remote Similarity NPC236338
0.6032 Remote Similarity NPC194871
0.6032 Remote Similarity NPC21998
0.6 Remote Similarity NPC51329
0.6 Remote Similarity NPC65353
0.6 Remote Similarity NPC151648
0.5962 Remote Similarity NPC68577
0.5957 Remote Similarity NPC147824
0.5938 Remote Similarity NPC470256
0.5909 Remote Similarity NPC217161
0.5854 Remote Similarity NPC234005
0.5849 Remote Similarity NPC223675
0.5846 Remote Similarity NPC88877
0.5846 Remote Similarity NPC476591
0.5833 Remote Similarity NPC309408
0.5818 Remote Similarity NPC191643
0.5818 Remote Similarity NPC151919
0.5789 Remote Similarity NPC478117
0.5778 Remote Similarity NPC122676
0.5769 Remote Similarity NPC87137
0.5763 Remote Similarity NPC189700
0.5741 Remote Similarity NPC27264
0.5735 Remote Similarity NPC48641
0.5672 Remote Similarity NPC163003
0.5667 Remote Similarity NPC133600
0.5667 Remote Similarity NPC286189
0.5645 Remote Similarity NPC68110
0.5645 Remote Similarity NPC473737
0.5636 Remote Similarity NPC148056
0.5625 Remote Similarity NPC248125
0.5625 Remote Similarity NPC200147

  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 NPC190649 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
0.5926 Remote Similarity NPD6927 Phase 3
0.5893 Remote Similarity NPD9298 Approved
0.5882 Remote Similarity NPD9378 Approved
0.5833 Remote Similarity NPD8839 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