Structure

Physi-Chem Properties

Molecular Weight:  162.07
Volume:  177.358
LogP:  2.933
LogD:  2.003
LogS:  -2.801
# Rotatable Bonds:  1
TPSA:  26.3
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.434
Synthetic Accessibility Score:  3.745
Fsp3:  0.3
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:  -4.306
MDCK Permeability:  2.662260340002831e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.009
20% Bioavailability (F20%):  0.97
30% Bioavailability (F30%):  0.994

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.876
Plasma Protein Binding (PPB):  97.54102325439453%
Volume Distribution (VD):  0.738
Pgp-substrate:  2.1482574939727783%

ADMET: Metabolism

CYP1A2-inhibitor:  0.973
CYP1A2-substrate:  0.256
CYP2C19-inhibitor:  0.961
CYP2C19-substrate:  0.718
CYP2C9-inhibitor:  0.893
CYP2C9-substrate:  0.866
CYP2D6-inhibitor:  0.05
CYP2D6-substrate:  0.359
CYP3A4-inhibitor:  0.79
CYP3A4-substrate:  0.218

ADMET: Excretion

Clearance (CL):  7.867
Half-life (T1/2):  0.695

ADMET: Toxicity

hERG Blockers:  0.0
Human Hepatotoxicity (H-HT):  0.989
Drug-inuced Liver Injury (DILI):  0.859
AMES Toxicity:  0.909
Rat Oral Acute Toxicity:  0.969
Maximum Recommended Daily Dose:  0.918
Skin Sensitization:  0.948
Carcinogencity:  0.869
Eye Corrosion:  0.949
Eye Irritation:  0.929
Respiratory Toxicity:  0.936

Download Data

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

  Natural Product: NPC82446

Natural Product ID:  NPC82446
Common Name*:   (4Z)-Lachnophyllum Lactone
IUPAC Name:   (5Z)-5-hex-2-ynylidenefuran-2-one
Synonyms:  
Standard InCHIKey:  PHUPYFCPQIPDNQ-TWGQIWQCSA-N
Standard InCHI:  InChI=1S/C10H10O2/c1-2-3-4-5-6-9-7-8-10(11)12-9/h6-8H,2-3H2,1H3/b9-6-
SMILES:  CCCC#C/C=C1/C=CC(=O)O1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2229361
PubChem CID:   5380634
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 = 0.3 mm PMID[512725]
NPT2241 Organism Glomerella acutata Glomerella acutata IZ = 0.75 mm PMID[512725]
NPT562 Organism Colletotrichum gloeosporioides Colletotrichum gloeosporioides IZ = 0.58 mm PMID[512725]
NPT854 Organism Lemna paucicostata Lemna paucicostata IC50 = 104000.0 nM PMID[512725]

☑ 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 NPC82446 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 NPC90490
0.7826 Intermediate Similarity NPC250954
0.7826 Intermediate Similarity NPC297608
0.78 Intermediate Similarity NPC128520
0.7368 Intermediate Similarity NPC189700
0.7234 Intermediate Similarity NPC147824
0.7222 Intermediate Similarity NPC191643
0.7119 Intermediate Similarity NPC130953
0.7111 Intermediate Similarity NPC122676
0.7083 Intermediate Similarity NPC281043
0.7018 Intermediate Similarity NPC86948
0.7018 Intermediate Similarity NPC150717
0.6981 Remote Similarity NPC126184
0.6981 Remote Similarity NPC234084
0.6949 Remote Similarity NPC133600
0.6842 Remote Similarity NPC173157
0.6833 Remote Similarity NPC98519
0.6724 Remote Similarity NPC221763
0.6719 Remote Similarity NPC225272
0.6667 Remote Similarity NPC218486
0.6667 Remote Similarity NPC159535
0.6667 Remote Similarity NPC103560
0.6667 Remote Similarity NPC151761
0.6667 Remote Similarity NPC63598
0.6613 Remote Similarity NPC474723
0.6613 Remote Similarity NPC474729
0.6552 Remote Similarity NPC474913
0.6552 Remote Similarity NPC478117
0.6471 Remote Similarity NPC102879
0.6471 Remote Similarity NPC41409
0.6441 Remote Similarity NPC245002
0.6406 Remote Similarity NPC220766
0.6379 Remote Similarity NPC151923
0.6379 Remote Similarity NPC269615
0.6379 Remote Similarity NPC9611
0.6349 Remote Similarity NPC179087
0.6349 Remote Similarity NPC132243
0.6349 Remote Similarity NPC44343
0.6349 Remote Similarity NPC473737
0.6349 Remote Similarity NPC210303
0.6333 Remote Similarity NPC474825
0.6316 Remote Similarity NPC106531
0.6308 Remote Similarity NPC191233
0.629 Remote Similarity NPC309408
0.6269 Remote Similarity NPC470693
0.625 Remote Similarity NPC275316
0.625 Remote Similarity NPC65353
0.625 Remote Similarity NPC15789
0.625 Remote Similarity NPC9290
0.623 Remote Similarity NPC474084
0.62 Remote Similarity NPC298413
0.617 Remote Similarity NPC63354
0.6154 Remote Similarity NPC57923
0.6122 Remote Similarity NPC107877
0.6119 Remote Similarity NPC287705
0.6094 Remote Similarity NPC2328
0.6066 Remote Similarity NPC223804
0.6042 Remote Similarity NPC60675
0.6042 Remote Similarity NPC297363
0.6032 Remote Similarity NPC429928
0.6 Remote Similarity NPC475618
0.5965 Remote Similarity NPC236338
0.5965 Remote Similarity NPC221467
0.5909 Remote Similarity NPC476589
0.5909 Remote Similarity NPC471566
0.5909 Remote Similarity NPC471565
0.5909 Remote Similarity NPC133904
0.5909 Remote Similarity NPC182794
0.5902 Remote Similarity NPC230296
0.5882 Remote Similarity NPC200147
0.5873 Remote Similarity NPC474588
0.5873 Remote Similarity NPC222852
0.5873 Remote Similarity NPC474711
0.5846 Remote Similarity NPC475073
0.5833 Remote Similarity NPC478120
0.5818 Remote Similarity NPC270706
0.5806 Remote Similarity NPC471279
0.5806 Remote Similarity NPC212730
0.5806 Remote Similarity NPC471277
0.5806 Remote Similarity NPC265551
0.5806 Remote Similarity NPC472445
0.5797 Remote Similarity NPC232812
0.5781 Remote Similarity NPC299730
0.5775 Remote Similarity NPC252503
0.5769 Remote Similarity NPC8270
0.5738 Remote Similarity NPC25038
0.5714 Remote Similarity NPC64234
0.5714 Remote Similarity NPC37929
0.5714 Remote Similarity NPC128280
0.5694 Remote Similarity NPC470686
0.5692 Remote Similarity NPC15193
0.5692 Remote Similarity NPC151648
0.5672 Remote Similarity NPC131174
0.5672 Remote Similarity NPC471556
0.5672 Remote Similarity NPC470688
0.566 Remote Similarity NPC159773
0.566 Remote Similarity NPC221250
0.5652 Remote Similarity NPC477117
0.5652 Remote Similarity NPC323552
0.5652 Remote Similarity NPC474823
0.5645 Remote Similarity NPC51846
0.5634 Remote Similarity NPC186531
0.5625 Remote Similarity NPC302564
0.5625 Remote Similarity NPC159650
0.5625 Remote Similarity NPC22897
0.5625 Remote Similarity NPC97570
0.5625 Remote Similarity NPC474267
0.5625 Remote Similarity NPC286189
0.5616 Remote Similarity NPC478195
0.5616 Remote Similarity NPC478193
0.5616 Remote Similarity NPC478192
0.5616 Remote Similarity NPC478196
0.5616 Remote Similarity NPC478194
0.5616 Remote Similarity NPC478191
0.56 Remote Similarity NPC308418

  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 NPC82446 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
0.6809 Remote Similarity NPD9115 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