Structure

Physi-Chem Properties

Molecular Weight:  186.01
Volume:  169.404
LogP:  1.395
LogD:  1.062
LogS:  -2.476
# Rotatable Bonds:  1
TPSA:  43.37
# H-Bond Aceptor:  3
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.578
Synthetic Accessibility Score:  2.835
Fsp3:  0.25
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  2

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.32
MDCK Permeability:  3.5118158848490566e-05
Pgp-inhibitor:  0.002
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.002
20% Bioavailability (F20%):  0.006
30% Bioavailability (F30%):  0.007

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.063
Plasma Protein Binding (PPB):  78.50533294677734%
Volume Distribution (VD):  1.14
Pgp-substrate:  13.792489051818848%

ADMET: Metabolism

CYP1A2-inhibitor:  0.98
CYP1A2-substrate:  0.937
CYP2C19-inhibitor:  0.88
CYP2C19-substrate:  0.796
CYP2C9-inhibitor:  0.483
CYP2C9-substrate:  0.359
CYP2D6-inhibitor:  0.871
CYP2D6-substrate:  0.102
CYP3A4-inhibitor:  0.142
CYP3A4-substrate:  0.231

ADMET: Excretion

Clearance (CL):  6.22
Half-life (T1/2):  0.519

ADMET: Toxicity

hERG Blockers:  0.008
Human Hepatotoxicity (H-HT):  0.77
Drug-inuced Liver Injury (DILI):  0.199
AMES Toxicity:  0.898
Rat Oral Acute Toxicity:  0.945
Maximum Recommended Daily Dose:  0.852
Skin Sensitization:  0.937
Carcinogencity:  0.893
Eye Corrosion:  0.928
Eye Irritation:  0.98
Respiratory Toxicity:  0.972

Download Data

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

  Natural Product: NPC168521

Natural Product ID:  NPC168521
Common Name*:   2-Chloro-5-Methoxy-3-Methylcyclohexa-2,5-Diene-1,4-Dione
IUPAC Name:   2-chloro-5-methoxy-3-methylcyclohexa-2,5-diene-1,4-dione
Synonyms:  
Standard InCHIKey:  SXCLPOXHBILXEY-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C8H7ClO3/c1-4-7(9)5(10)3-6(12-2)8(4)11/h3H,1-2H3
SMILES:  COC1=CC(=O)C(=C(C1=O)C)Cl
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL253141
PubChem CID:   23634447
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0001831] Carbonyl compounds
          • [CHEMONTID:0000118] Ketones
            • [CHEMONTID:0003487] Cyclic ketones
              • [CHEMONTID:0002495] Quinones
                • [CHEMONTID:0002384] Benzoquinones
                  • [CHEMONTID:0002494] P-benzoquinones

*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
NPO33440 Xylaria sp. Species Xylariaceae Eukaryota n.a. n.a. n.a. PMID[15921427]
NPO33440 Xylaria sp. Species Xylariaceae Eukaryota n.a. n.a. n.a. PMID[17892262]
NPO33440 Xylaria sp. Species Xylariaceae Eukaryota n.a. n.a. n.a. PMID[18500842]
NPO33440 Xylaria sp. Species Xylariaceae Eukaryota Isolated from the lichen Leptogium saturninum (Dicks.) Nyl. Zixi Mountain, Yunnan, China 2006-NOV PMID[21428374]

☑ 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
NPT189 Cell Line Vero Chlorocebus aethiops IC50 = 1350.0 nM PMID[547819]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 1840.0 nM PMID[547819]

☑ 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 NPC168521 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
0.8627 High Similarity NPC220191
0.8462 Intermediate Similarity NPC22329
0.8148 Intermediate Similarity NPC474805
0.7679 Intermediate Similarity NPC317796
0.7679 Intermediate Similarity NPC129710
0.7647 Intermediate Similarity NPC106547
0.75 Intermediate Similarity NPC110396
0.7458 Intermediate Similarity NPC139056
0.7333 Intermediate Similarity NPC473494
0.7288 Intermediate Similarity NPC200831
0.7288 Intermediate Similarity NPC224103
0.7288 Intermediate Similarity NPC299369
0.7018 Intermediate Similarity NPC137396
0.6984 Remote Similarity NPC57463
0.6984 Remote Similarity NPC151728
0.6875 Remote Similarity NPC34622
0.6875 Remote Similarity NPC474400
0.6863 Remote Similarity NPC111474
0.6769 Remote Similarity NPC98897
0.6667 Remote Similarity NPC16119
0.6567 Remote Similarity NPC474619
0.6567 Remote Similarity NPC251429
0.6567 Remote Similarity NPC243272
0.6567 Remote Similarity NPC298249
0.6545 Remote Similarity NPC158853
0.6471 Remote Similarity NPC125578
0.6471 Remote Similarity NPC146376
0.6471 Remote Similarity NPC134385
0.6471 Remote Similarity NPC263382
0.6377 Remote Similarity NPC262673
0.6377 Remote Similarity NPC94488
0.6364 Remote Similarity NPC477686
0.6349 Remote Similarity NPC320421
0.6286 Remote Similarity NPC94743
0.6286 Remote Similarity NPC291062
0.625 Remote Similarity NPC191337
0.625 Remote Similarity NPC166788
0.6197 Remote Similarity NPC474539
0.6129 Remote Similarity NPC25038
0.6102 Remote Similarity NPC107703
0.6061 Remote Similarity NPC68044
0.6027 Remote Similarity NPC264178
0.6027 Remote Similarity NPC147438
0.6 Remote Similarity NPC203233
0.6 Remote Similarity NPC134593
0.597 Remote Similarity NPC143168
0.597 Remote Similarity NPC477830
0.597 Remote Similarity NPC53109
0.5938 Remote Similarity NPC474825
0.5902 Remote Similarity NPC46565
0.5902 Remote Similarity NPC229046
0.5882 Remote Similarity NPC269641
0.5882 Remote Similarity NPC7029
0.5882 Remote Similarity NPC475618
0.5867 Remote Similarity NPC26504
0.5846 Remote Similarity NPC281195
0.5833 Remote Similarity NPC15325
0.5833 Remote Similarity NPC118788
0.5833 Remote Similarity NPC224270
0.5833 Remote Similarity NPC228776
0.58 Remote Similarity NPC304788
0.5789 Remote Similarity NPC25771
0.5789 Remote Similarity NPC471753
0.5789 Remote Similarity NPC473536
0.5789 Remote Similarity NPC75134
0.5781 Remote Similarity NPC150717
0.5758 Remote Similarity NPC133600
0.5753 Remote Similarity NPC66365
0.5692 Remote Similarity NPC268185
0.5686 Remote Similarity NPC12889
0.5672 Remote Similarity NPC79756
0.5672 Remote Similarity NPC309408
0.5645 Remote Similarity NPC191643
0.5636 Remote Similarity NPC101147
0.5636 Remote Similarity NPC2741
0.5625 Remote Similarity NPC297280
0.5625 Remote Similarity NPC173157
0.5614 Remote Similarity NPC292463
0.5614 Remote Similarity NPC216921

  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 NPC168521 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
0.7288 Intermediate Similarity NPD8779 Phase 3
0.6923 Remote Similarity NPD9297 Discontinued
0.6923 Remote Similarity NPD9091 Suspended
0.6667 Remote Similarity NPD6108 Clinical (unspecified phase)
0.6545 Remote Similarity NPD9090 Phase 3
0.597 Remote Similarity NPD2664 Clinical (unspecified phase)
0.5942 Remote Similarity NPD3704 Approved
0.5789 Remote Similarity NPD4756 Discovery

  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