Structure

Physi-Chem Properties

Molecular Weight:  156.04
Volume:  142.403
LogP:  -0.742
LogD:  -1.521
LogS:  -0.95
# Rotatable Bonds:  1
TPSA:  66.9
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.489
Synthetic Accessibility Score:  4.371
Fsp3:  0.714
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.72
MDCK Permeability:  0.0001971909950952977
Pgp-inhibitor:  0.023
Pgp-substrate:  0.013
Human Intestinal Absorption (HIA):  0.009
20% Bioavailability (F20%):  0.04
30% Bioavailability (F30%):  0.002

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.224
Plasma Protein Binding (PPB):  23.63761329650879%
Volume Distribution (VD):  0.97
Pgp-substrate:  83.57755279541016%

ADMET: Metabolism

CYP1A2-inhibitor:  0.022
CYP1A2-substrate:  0.278
CYP2C19-inhibitor:  0.02
CYP2C19-substrate:  0.175
CYP2C9-inhibitor:  0.004
CYP2C9-substrate:  0.115
CYP2D6-inhibitor:  0.004
CYP2D6-substrate:  0.195
CYP3A4-inhibitor:  0.004
CYP3A4-substrate:  0.13

ADMET: Excretion

Clearance (CL):  7.407
Half-life (T1/2):  0.857

ADMET: Toxicity

hERG Blockers:  0.093
Human Hepatotoxicity (H-HT):  0.103
Drug-inuced Liver Injury (DILI):  0.833
AMES Toxicity:  0.075
Rat Oral Acute Toxicity:  0.809
Maximum Recommended Daily Dose:  0.015
Skin Sensitization:  0.39
Carcinogencity:  0.272
Eye Corrosion:  0.96
Eye Irritation:  0.941
Respiratory Toxicity:  0.071

Download Data

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

  Natural Product: NPC253364

Natural Product ID:  NPC253364
Common Name*:   Parasitenone
IUPAC Name:   (1S,2S,6S)-2-hydroxy-3-(hydroxymethyl)-7-oxabicyclo[4.1.0]hept-3-en-5-one
Synonyms:   Parasitenone
Standard InCHIKey:  RZGZRGXCPXHJFW-XVMARJQXSA-N
Standard InCHI:  InChI=1S/C7H8O4/c8-2-3-1-4(9)6-7(11-6)5(3)10/h1,5-8,10H,2H2/t5-,6+,7-/m0/s1
SMILES:  OCC1=CC(=O)[C@@H]2[C@H]([C@H]1O)O2
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL493204
PubChem CID:   636767
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:0004325] Cyclohexenones

*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
NPO23190 Aspergillus parasiticus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[11678666]
NPO23190 Aspergillus parasiticus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[12027772]
NPO23190 Aspergillus parasiticus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[15184162]
NPO23190 Aspergillus parasiticus Species Aspergillaceae Eukaryota n.a. latex n.a. PMID[21854017]
NPO23190 Aspergillus parasiticus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[22103394]
NPO23190 Aspergillus parasiticus Species Aspergillaceae Eukaryota n.a. n.a. n.a. PMID[24738739]
NPO23190 Aspergillus parasiticus Species Aspergillaceae 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
NPT1 Others Radical scavenging activity IC50 = 57000.0 nM PMID[449033]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 52600.0 nM PMID[449033]

☑ 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 NPC253364 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
0.961 High Similarity NPC159714
0.961 High Similarity NPC221510
0.925 High Similarity NPC469809
0.8846 High Similarity NPC272267
0.8537 High Similarity NPC47450
0.814 Intermediate Similarity NPC196381
0.8085 Intermediate Similarity NPC39996
0.8 Intermediate Similarity NPC118902
0.8 Intermediate Similarity NPC104161
0.8 Intermediate Similarity NPC469980
0.7978 Intermediate Similarity NPC477684
0.7755 Intermediate Similarity NPC266514
0.7711 Intermediate Similarity NPC141195
0.7711 Intermediate Similarity NPC47844
0.7609 Intermediate Similarity NPC327620
0.76 Intermediate Similarity NPC87335
0.7564 Intermediate Similarity NPC472072
0.7526 Intermediate Similarity NPC478176
0.75 Intermediate Similarity NPC473536
0.7423 Intermediate Similarity NPC112613
0.7423 Intermediate Similarity NPC207885
0.7416 Intermediate Similarity NPC187529
0.7349 Intermediate Similarity NPC24590
0.7327 Intermediate Similarity NPC264819
0.7312 Intermediate Similarity NPC327760
0.7312 Intermediate Similarity NPC6099
0.7312 Intermediate Similarity NPC303230
0.7312 Intermediate Similarity NPC114345
0.7292 Intermediate Similarity NPC471916
0.7282 Intermediate Similarity NPC317107
0.7253 Intermediate Similarity NPC472007
0.7222 Intermediate Similarity NPC77971
0.7212 Intermediate Similarity NPC317687
0.7188 Intermediate Similarity NPC279722
0.7184 Intermediate Similarity NPC89408
0.7176 Intermediate Similarity NPC474197
0.7159 Intermediate Similarity NPC67254
0.7143 Intermediate Similarity NPC472009
0.7128 Intermediate Similarity NPC475441
0.7128 Intermediate Similarity NPC476705
0.7111 Intermediate Similarity NPC316819
0.7041 Intermediate Similarity NPC475284
0.7041 Intermediate Similarity NPC306908
0.7041 Intermediate Similarity NPC281608
0.7021 Intermediate Similarity NPC471399
0.7011 Intermediate Similarity NPC68119
0.7011 Intermediate Similarity NPC13823
0.701 Intermediate Similarity NPC94337
0.7 Intermediate Similarity NPC477784
0.7 Intermediate Similarity NPC477786
0.7 Intermediate Similarity NPC477785
0.699 Remote Similarity NPC322903
0.6989 Remote Similarity NPC472008
0.6988 Remote Similarity NPC107848
0.6947 Remote Similarity NPC142838
0.6941 Remote Similarity NPC474545
0.6939 Remote Similarity NPC236176
0.6939 Remote Similarity NPC20066
0.6931 Remote Similarity NPC131366
0.6923 Remote Similarity NPC474251
0.6916 Remote Similarity NPC80650
0.69 Remote Similarity NPC164598
0.69 Remote Similarity NPC474339
0.6897 Remote Similarity NPC82666
0.6897 Remote Similarity NPC97173
0.6882 Remote Similarity NPC471738
0.6882 Remote Similarity NPC23622
0.6875 Remote Similarity NPC475221
0.6869 Remote Similarity NPC300584
0.6842 Remote Similarity NPC274075
0.6829 Remote Similarity NPC251429
0.6818 Remote Similarity NPC318481
0.6813 Remote Similarity NPC185256
0.6809 Remote Similarity NPC476707
0.6809 Remote Similarity NPC476706
0.6804 Remote Similarity NPC121825
0.68 Remote Similarity NPC324667
0.68 Remote Similarity NPC475949
0.6792 Remote Similarity NPC476023
0.6771 Remote Similarity NPC146852
0.6744 Remote Similarity NPC326504
0.6742 Remote Similarity NPC291260
0.6737 Remote Similarity NPC473100
0.6737 Remote Similarity NPC14901
0.6737 Remote Similarity NPC130359
0.6731 Remote Similarity NPC469853
0.6701 Remote Similarity NPC469692
0.6701 Remote Similarity NPC469645
0.6701 Remote Similarity NPC61275
0.67 Remote Similarity NPC35717
0.67 Remote Similarity NPC161855
0.6698 Remote Similarity NPC115257
0.6698 Remote Similarity NPC161816
0.6667 Remote Similarity NPC14862
0.6667 Remote Similarity NPC470947
0.6667 Remote Similarity NPC307126
0.6667 Remote Similarity NPC162741
0.6667 Remote Similarity NPC473099
0.6667 Remote Similarity NPC473291
0.6667 Remote Similarity NPC470945
0.6667 Remote Similarity NPC68303
0.6667 Remote Similarity NPC327106
0.6667 Remote Similarity NPC470946
0.6667 Remote Similarity NPC182383
0.6667 Remote Similarity NPC469464
0.6667 Remote Similarity NPC474664
0.6667 Remote Similarity NPC91332
0.6667 Remote Similarity NPC473582
0.6667 Remote Similarity NPC471148
0.6667 Remote Similarity NPC233379
0.6636 Remote Similarity NPC477116
0.6636 Remote Similarity NPC27999
0.6633 Remote Similarity NPC196227
0.6632 Remote Similarity NPC87189
0.6632 Remote Similarity NPC228415
0.6632 Remote Similarity NPC150063
0.6632 Remote Similarity NPC287089
0.6632 Remote Similarity NPC119740
0.6629 Remote Similarity NPC478122
0.6609 Remote Similarity NPC225049
0.6604 Remote Similarity NPC15218
0.6604 Remote Similarity NPC475922
0.6604 Remote Similarity NPC471400
0.6604 Remote Similarity NPC77089
0.6602 Remote Similarity NPC473624
0.6602 Remote Similarity NPC472755
0.66 Remote Similarity NPC474194
0.6598 Remote Similarity NPC116726
0.6596 Remote Similarity NPC47937
0.6596 Remote Similarity NPC262026
0.6596 Remote Similarity NPC204686
0.6596 Remote Similarity NPC210218
0.6596 Remote Similarity NPC134807
0.6596 Remote Similarity NPC308412
0.6596 Remote Similarity NPC219498
0.6596 Remote Similarity NPC473687
0.6596 Remote Similarity NPC134885
0.6593 Remote Similarity NPC297440
0.6591 Remote Similarity NPC190400
0.6591 Remote Similarity NPC477708
0.6591 Remote Similarity NPC49392
0.6588 Remote Similarity NPC202011
0.6577 Remote Similarity NPC251310
0.6574 Remote Similarity NPC473877
0.6571 Remote Similarity NPC194620
0.6571 Remote Similarity NPC477513
0.6571 Remote Similarity NPC324327
0.6571 Remote Similarity NPC474421
0.6571 Remote Similarity NPC72813
0.6571 Remote Similarity NPC326994
0.6571 Remote Similarity NPC474716
0.6569 Remote Similarity NPC185141
0.6569 Remote Similarity NPC133907
0.6569 Remote Similarity NPC476270
0.6569 Remote Similarity NPC472753
0.6569 Remote Similarity NPC46998
0.6569 Remote Similarity NPC128733
0.6569 Remote Similarity NPC201718
0.6569 Remote Similarity NPC110443
0.6566 Remote Similarity NPC227494
0.6559 Remote Similarity NPC32676
0.6552 Remote Similarity NPC473489
0.6538 Remote Similarity NPC474741
0.6538 Remote Similarity NPC472756
0.6535 Remote Similarity NPC177232
0.6535 Remote Similarity NPC471144
0.6535 Remote Similarity NPC470541
0.6535 Remote Similarity NPC212465
0.6531 Remote Similarity NPC288240
0.6531 Remote Similarity NPC162205
0.6531 Remote Similarity NPC295204
0.6531 Remote Similarity NPC273579
0.6526 Remote Similarity NPC179659
0.6526 Remote Similarity NPC178215
0.6522 Remote Similarity NPC11383
0.6522 Remote Similarity NPC475046
0.6522 Remote Similarity NPC310450
0.6522 Remote Similarity NPC474959
0.6517 Remote Similarity NPC471061
0.6517 Remote Similarity NPC475711
0.6514 Remote Similarity NPC477266
0.6509 Remote Similarity NPC327286
0.6509 Remote Similarity NPC55972
0.6509 Remote Similarity NPC169888
0.6505 Remote Similarity NPC472754
0.65 Remote Similarity NPC477921
0.6495 Remote Similarity NPC474232
0.6495 Remote Similarity NPC131864
0.6489 Remote Similarity NPC1083
0.6489 Remote Similarity NPC132496
0.6489 Remote Similarity NPC286338
0.6489 Remote Similarity NPC110710
0.6489 Remote Similarity NPC107986
0.6489 Remote Similarity NPC82795
0.6489 Remote Similarity NPC473651
0.6489 Remote Similarity NPC103284
0.6489 Remote Similarity NPC15807
0.6489 Remote Similarity NPC473478
0.6489 Remote Similarity NPC473669
0.6489 Remote Similarity NPC223871

  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 NPC253364 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
0.6813 Remote Similarity NPD6110 Phase 1
0.6667 Remote Similarity NPD46 Approved
0.6667 Remote Similarity NPD6698 Approved
0.6333 Remote Similarity NPD4756 Discovery
0.631 Remote Similarity NPD3704 Approved
0.6263 Remote Similarity NPD7983 Approved
0.6222 Remote Similarity NPD818 Approved
0.6222 Remote Similarity NPD819 Approved
0.6214 Remote Similarity NPD4225 Approved
0.6195 Remote Similarity NPD7115 Discovery
0.6139 Remote Similarity NPD5282 Discontinued
0.6095 Remote Similarity NPD5344 Discontinued
0.6091 Remote Similarity NPD6371 Approved
0.604 Remote Similarity NPD5779 Approved
0.604 Remote Similarity NPD5778 Approved
0.6 Remote Similarity NPD7838 Discovery
0.5963 Remote Similarity NPD7899 Clinical (unspecified phase)
0.5952 Remote Similarity NPD2664 Clinical (unspecified phase)
0.5904 Remote Similarity NPD9120 Clinical (unspecified phase)
0.5897 Remote Similarity NPD6319 Approved
0.5882 Remote Similarity NPD8328 Phase 3
0.5816 Remote Similarity NPD1696 Phase 3
0.5804 Remote Similarity NPD4634 Approved
0.5789 Remote Similarity NPD8259 Clinical (unspecified phase)
0.5763 Remote Similarity NPD6054 Approved
0.5763 Remote Similarity NPD6059 Approved
0.5752 Remote Similarity NPD7601 Clinical (unspecified phase)
0.5747 Remote Similarity NPD6108 Clinical (unspecified phase)
0.5732 Remote Similarity NPD8959 Approved
0.5714 Remote Similarity NPD8516 Approved
0.5714 Remote Similarity NPD4061 Clinical (unspecified phase)
0.5714 Remote Similarity NPD8513 Phase 3
0.5714 Remote Similarity NPD6016 Approved
0.5714 Remote Similarity NPD6015 Approved
0.5714 Remote Similarity NPD8515 Approved
0.5714 Remote Similarity NPD8517 Approved
0.5701 Remote Similarity NPD6648 Approved
0.5667 Remote Similarity NPD5988 Approved
0.5667 Remote Similarity NPD6370 Approved
0.5657 Remote Similarity NPD5363 Approved
0.5619 Remote Similarity NPD1698 Clinical (unspecified phase)
0.5614 Remote Similarity NPD8413 Clinical (unspecified phase)
0.5607 Remote Similarity NPD8029 Clinical (unspecified phase)

  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