Structure

Physi-Chem Properties

Molecular Weight:  160.05
Volume:  174.722
LogP:  2.599
LogD:  1.698
LogS:  -2.528
# Rotatable Bonds:  0
TPSA:  26.3
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.397
Synthetic Accessibility Score:  4.198
Fsp3:  0.1
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:  -4.384
MDCK Permeability:  2.0331899577286094e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.022
20% Bioavailability (F20%):  0.91
30% Bioavailability (F30%):  0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.633
Plasma Protein Binding (PPB):  98.2042465209961%
Volume Distribution (VD):  0.671
Pgp-substrate:  2.6896238327026367%

ADMET: Metabolism

CYP1A2-inhibitor:  0.983
CYP1A2-substrate:  0.137
CYP2C19-inhibitor:  0.96
CYP2C19-substrate:  0.637
CYP2C9-inhibitor:  0.888
CYP2C9-substrate:  0.07
CYP2D6-inhibitor:  0.308
CYP2D6-substrate:  0.095
CYP3A4-inhibitor:  0.868
CYP3A4-substrate:  0.318

ADMET: Excretion

Clearance (CL):  10.421
Half-life (T1/2):  0.756

ADMET: Toxicity

hERG Blockers:  0.0
Human Hepatotoxicity (H-HT):  0.993
Drug-inuced Liver Injury (DILI):  0.966
AMES Toxicity:  0.944
Rat Oral Acute Toxicity:  0.969
Maximum Recommended Daily Dose:  0.912
Skin Sensitization:  0.95
Carcinogencity:  0.864
Eye Corrosion:  0.96
Eye Irritation:  0.955
Respiratory Toxicity:  0.939

Download Data

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

  Natural Product: NPC90490

Natural Product ID:  NPC90490
Common Name*:   (4Z,8Z)-Matricaria Lactone
IUPAC Name:   (5Z)-5-[(Z)-hex-4-en-2-ynylidene]furan-2-one
Synonyms:  
Standard InCHIKey:  ZNOFNADHELRFDF-CITLEARMSA-N
Standard InCHI:  InChI=1S/C10H8O2/c1-2-3-4-5-6-9-7-8-10(11)12-9/h2-3,6-8H,1H3/b3-2-,9-6-
SMILES:  C/C=CC#C/C=C/1OC(=O)C=C1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2229363
PubChem CID:   6277481
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001983] Dihydrofurans
        • [CHEMONTID:0001982] Furanones
          • [CHEMONTID:0002223] Butenolides

*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
NPO12088 Conyza canadensis Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[20121251]
NPO12088 Conyza canadensis Species Asteraceae Eukaryota n.a. n.a. n.a. PMID[22612410]
NPO12088 Conyza canadensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12088 Conyza canadensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12088 Conyza canadensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO12088 Conyza canadensis Species Asteraceae 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
NPT851 Organism Colletotrichum fragariae Colletotrichum fragariae IZ = 2.65 mm PMID[521577]
NPT2241 Organism Glomerella acutata Glomerella acutata IZ = 0.7 mm PMID[521577]
NPT562 Organism Colletotrichum gloeosporioides Colletotrichum gloeosporioides IZ = 0.98 mm PMID[521577]
NPT854 Organism Lemna paucicostata Lemna paucicostata IC50 = 220000.0 nM PMID[521577]

☑ 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 NPC90490 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
0.9778 High Similarity NPC82446
0.8 Intermediate Similarity NPC297608
0.7959 Intermediate Similarity NPC128520
0.7609 Intermediate Similarity NPC250954
0.75 Intermediate Similarity NPC189700
0.7391 Intermediate Similarity NPC147824
0.7358 Intermediate Similarity NPC191643
0.7273 Intermediate Similarity NPC122676
0.7241 Intermediate Similarity NPC130953
0.7234 Intermediate Similarity NPC281043
0.7143 Intermediate Similarity NPC86948
0.7143 Intermediate Similarity NPC150717
0.7115 Intermediate Similarity NPC234084
0.7115 Intermediate Similarity NPC126184
0.7069 Intermediate Similarity NPC133600
0.6964 Remote Similarity NPC173157
0.6949 Remote Similarity NPC98519
0.6842 Remote Similarity NPC221763
0.6809 Remote Similarity NPC63598
0.68 Remote Similarity NPC103560
0.6786 Remote Similarity NPC151761
0.6786 Remote Similarity NPC159535
0.6786 Remote Similarity NPC218486
0.6721 Remote Similarity NPC474723
0.6721 Remote Similarity NPC474729
0.6667 Remote Similarity NPC478117
0.66 Remote Similarity NPC41409
0.66 Remote Similarity NPC102879
0.6562 Remote Similarity NPC225272
0.6552 Remote Similarity NPC245002
0.6508 Remote Similarity NPC220766
0.6491 Remote Similarity NPC151923
0.6491 Remote Similarity NPC9611
0.6452 Remote Similarity NPC473737
0.6452 Remote Similarity NPC179087
0.6452 Remote Similarity NPC132243
0.6452 Remote Similarity NPC210303
0.6452 Remote Similarity NPC44343
0.6441 Remote Similarity NPC474825
0.6429 Remote Similarity NPC106531
0.6406 Remote Similarity NPC191233
0.6393 Remote Similarity NPC309408
0.6383 Remote Similarity NPC65353
0.6383 Remote Similarity NPC9290
0.6379 Remote Similarity NPC474913
0.6364 Remote Similarity NPC275316
0.6364 Remote Similarity NPC15789
0.6364 Remote Similarity NPC470693
0.6333 Remote Similarity NPC474084
0.6327 Remote Similarity NPC298413
0.6304 Remote Similarity NPC63354
0.6275 Remote Similarity NPC57923
0.625 Remote Similarity NPC107877
0.6212 Remote Similarity NPC287705
0.6207 Remote Similarity NPC269615
0.619 Remote Similarity NPC2328
0.617 Remote Similarity NPC297363
0.617 Remote Similarity NPC60675
0.6167 Remote Similarity NPC223804
0.6129 Remote Similarity NPC429928
0.6094 Remote Similarity NPC475618
0.6071 Remote Similarity NPC236338
0.6071 Remote Similarity NPC221467
0.6 Remote Similarity NPC200147
0.6 Remote Similarity NPC133904
0.6 Remote Similarity NPC230296
0.6 Remote Similarity NPC471565
0.6 Remote Similarity NPC476589
0.6 Remote Similarity NPC471566
0.6 Remote Similarity NPC182794
0.5968 Remote Similarity NPC474711
0.5968 Remote Similarity NPC222852
0.5968 Remote Similarity NPC474588
0.5938 Remote Similarity NPC475073
0.5932 Remote Similarity NPC478120
0.5926 Remote Similarity NPC270706
0.5882 Remote Similarity NPC8270
0.5882 Remote Similarity NPC232812
0.5857 Remote Similarity NPC252503
0.5833 Remote Similarity NPC25038
0.5818 Remote Similarity NPC128280
0.5797 Remote Similarity NPC64234
0.5797 Remote Similarity NPC37929
0.5781 Remote Similarity NPC151648
0.5781 Remote Similarity NPC15193
0.5778 Remote Similarity NPC323552
0.5775 Remote Similarity NPC470686
0.5769 Remote Similarity NPC159773
0.5769 Remote Similarity NPC221250
0.5758 Remote Similarity NPC471556
0.5758 Remote Similarity NPC131174
0.5758 Remote Similarity NPC470688
0.5738 Remote Similarity NPC51846
0.5735 Remote Similarity NPC477117
0.5735 Remote Similarity NPC474823
0.5714 Remote Similarity NPC97570
0.5714 Remote Similarity NPC308418
0.5714 Remote Similarity NPC286189
0.5714 Remote Similarity NPC302564
0.5714 Remote Similarity NPC159650
0.5714 Remote Similarity NPC22897
0.5694 Remote Similarity NPC478193
0.5694 Remote Similarity NPC478195
0.5694 Remote Similarity NPC478192
0.5694 Remote Similarity NPC478194
0.5694 Remote Similarity NPC478196
0.5694 Remote Similarity NPC478191
0.569 Remote Similarity NPC43053
0.5672 Remote Similarity NPC315115
0.5672 Remote Similarity NPC146811
0.5672 Remote Similarity NPC276299
0.5672 Remote Similarity NPC37382
0.5652 Remote Similarity NPC475004
0.5645 Remote Similarity NPC44542
0.5645 Remote Similarity NPC471279
0.5645 Remote Similarity NPC472445
0.5645 Remote Similarity NPC265551
0.5645 Remote Similarity NPC129150
0.5645 Remote Similarity NPC294938
0.5645 Remote Similarity NPC212730
0.5645 Remote Similarity NPC471277
0.5636 Remote Similarity NPC47946
0.5636 Remote Similarity NPC26600
0.5625 Remote Similarity NPC146507
0.5625 Remote Similarity NPC26223
0.5625 Remote Similarity NPC299730
0.5625 Remote Similarity NPC310810
0.5625 Remote Similarity NPC224651
0.5625 Remote Similarity NPC98098
0.5614 Remote Similarity NPC15912
0.5606 Remote Similarity NPC173409
0.5606 Remote Similarity NPC90463
0.5606 Remote Similarity NPC471611
0.5606 Remote Similarity NPC53136

  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 NPC90490 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
0.6957 Remote Similarity NPD9115 Approved
0.5625 Remote Similarity NPD8573 Approved
0.5614 Remote Similarity NPD4220 Pre-registration

  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