Structure

Physi-Chem Properties

Molecular Weight:  356.2
Volume:  374.384
LogP:  5.672
LogD:  4.35
LogS:  -5.987
# Rotatable Bonds:  13
TPSA:  48.67
# H-Bond Aceptor:  4
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.466
Synthetic Accessibility Score:  2.618
Fsp3:  0.737
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.607
MDCK Permeability:  2.174280416511465e-05
Pgp-inhibitor:  0.926
Pgp-substrate:  0.012
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.407
Plasma Protein Binding (PPB):  99.020263671875%
Volume Distribution (VD):  2.223
Pgp-substrate:  1.7141642570495605%

ADMET: Metabolism

CYP1A2-inhibitor:  0.894
CYP1A2-substrate:  0.909
CYP2C19-inhibitor:  0.869
CYP2C19-substrate:  0.831
CYP2C9-inhibitor:  0.811
CYP2C9-substrate:  0.918
CYP2D6-inhibitor:  0.025
CYP2D6-substrate:  0.839
CYP3A4-inhibitor:  0.594
CYP3A4-substrate:  0.167

ADMET: Excretion

Clearance (CL):  4.622
Half-life (T1/2):  0.12

ADMET: Toxicity

hERG Blockers:  0.027
Human Hepatotoxicity (H-HT):  0.856
Drug-inuced Liver Injury (DILI):  0.938
AMES Toxicity:  0.016
Rat Oral Acute Toxicity:  0.039
Maximum Recommended Daily Dose:  0.02
Skin Sensitization:  0.907
Carcinogencity:  0.11
Eye Corrosion:  0.005
Eye Irritation:  0.215
Respiratory Toxicity:  0.209

Download Data

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

  Natural Product: NPC261732

Natural Product ID:  NPC261732
Common Name*:   Lehualide I
IUPAC Name:   3,4-dimethoxy-5-methyl-6-(10-methylsulfanyldecyl)pyran-2-one
Synonyms:   Lehualide I
Standard InCHIKey:  KEAOWFVPPJUFOW-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C19H32O4S/c1-15-16(23-19(20)18(22-3)17(15)21-2)13-11-9-7-5-6-8-10-12-14-24-4/h5-14H2,1-4H3
SMILES:  Cc1c(CCCCCCCCCCSC)oc(=O)c(c1OC)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1773933
PubChem CID:   52952639
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000086] Pyrans
        • [CHEMONTID:0000481] Pyranones 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
NPO31509 Plakortis Genus Plakinidae Eukaryota n.a. Hawaiian n.a. PMID[16180823]
NPO31509 Plakortis Genus Plakinidae Eukaryota n.a. n.a. n.a. PMID[21351759]

☑ 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 = 10800.0 nM PMID[556282]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae GI = 67.0 % PMID[556282]

☑ 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 NPC261732 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
0.9859 High Similarity NPC47069
0.7 Intermediate Similarity NPC66365
0.6667 Remote Similarity NPC64234
0.6667 Remote Similarity NPC315285
0.6667 Remote Similarity NPC37929
0.6625 Remote Similarity NPC134593
0.6588 Remote Similarity NPC471225
0.6579 Remote Similarity NPC429928
0.6543 Remote Similarity NPC232812
0.6538 Remote Similarity NPC477457
0.6538 Remote Similarity NPC477456
0.6512 Remote Similarity NPC315765
0.65 Remote Similarity NPC132286
0.6463 Remote Similarity NPC315597
0.6463 Remote Similarity NPC316029
0.6456 Remote Similarity NPC471556
0.642 Remote Similarity NPC313444
0.642 Remote Similarity NPC475760
0.642 Remote Similarity NPC238223
0.642 Remote Similarity NPC134385
0.6395 Remote Similarity NPC315394
0.6282 Remote Similarity NPC15193
0.6277 Remote Similarity NPC142159
0.6277 Remote Similarity NPC95364
0.6267 Remote Similarity NPC86948
0.625 Remote Similarity NPC248193
0.625 Remote Similarity NPC271632
0.6224 Remote Similarity NPC173329
0.6224 Remote Similarity NPC288350
0.6207 Remote Similarity NPC316324
0.619 Remote Similarity NPC475762
0.6173 Remote Similarity NPC315115
0.6173 Remote Similarity NPC191233
0.6163 Remote Similarity NPC329826
0.6163 Remote Similarity NPC469414
0.6154 Remote Similarity NPC26223
0.6154 Remote Similarity NPC288281
0.6154 Remote Similarity NPC299730
0.6154 Remote Similarity NPC475714
0.6146 Remote Similarity NPC193396
0.6146 Remote Similarity NPC166110
0.6146 Remote Similarity NPC32944
0.6145 Remote Similarity NPC473277
0.6145 Remote Similarity NPC470693
0.6098 Remote Similarity NPC472266
0.6092 Remote Similarity NPC301525
0.6087 Remote Similarity NPC475706
0.6071 Remote Similarity NPC469660
0.6053 Remote Similarity NPC221763
0.6049 Remote Similarity NPC471565
0.6049 Remote Similarity NPC471566
0.6049 Remote Similarity NPC182794
0.6049 Remote Similarity NPC220766
0.6049 Remote Similarity NPC476589
0.6044 Remote Similarity NPC471326
0.6044 Remote Similarity NPC221231
0.6036 Remote Similarity NPC315974
0.6026 Remote Similarity NPC159650
0.6026 Remote Similarity NPC22897
0.6024 Remote Similarity NPC79220
0.6023 Remote Similarity NPC475711
0.6023 Remote Similarity NPC180290
0.6022 Remote Similarity NPC67081
0.6022 Remote Similarity NPC471223
0.6 Remote Similarity NPC133098
0.6 Remote Similarity NPC181587
0.6 Remote Similarity NPC84038
0.6 Remote Similarity NPC47653
0.598 Remote Similarity NPC471699
0.5957 Remote Similarity NPC291712
0.5955 Remote Similarity NPC248775
0.5952 Remote Similarity NPC475004
0.5949 Remote Similarity NPC79756
0.593 Remote Similarity NPC185186
0.593 Remote Similarity NPC474705
0.593 Remote Similarity NPC327383
0.593 Remote Similarity NPC329914
0.593 Remote Similarity NPC329890
0.593 Remote Similarity NPC144419
0.5926 Remote Similarity NPC148233
0.5926 Remote Similarity NPC308457
0.5926 Remote Similarity NPC25747
0.5921 Remote Similarity NPC173157
0.5918 Remote Similarity NPC475098
0.5918 Remote Similarity NPC189651
0.5914 Remote Similarity NPC474251
0.5904 Remote Similarity NPC474619
0.5895 Remote Similarity NPC125925
0.5895 Remote Similarity NPC45409
0.5889 Remote Similarity NPC180725
0.5889 Remote Similarity NPC1180
0.5889 Remote Similarity NPC470149
0.5889 Remote Similarity NPC470148
0.5889 Remote Similarity NPC471537
0.5882 Remote Similarity NPC473361
0.5882 Remote Similarity NPC329904
0.587 Remote Similarity NPC474028
0.587 Remote Similarity NPC10080
0.587 Remote Similarity NPC123908
0.587 Remote Similarity NPC474439
0.5862 Remote Similarity NPC470686
0.5862 Remote Similarity NPC107654
0.5862 Remote Similarity NPC477204
0.5854 Remote Similarity NPC98897
0.5851 Remote Similarity NPC99395
0.5851 Remote Similarity NPC281172
0.5851 Remote Similarity NPC197903
0.5844 Remote Similarity NPC150717
0.5843 Remote Similarity NPC54996
0.5843 Remote Similarity NPC473825
0.5843 Remote Similarity NPC474026
0.5833 Remote Similarity NPC475739
0.5833 Remote Similarity NPC218477
0.5833 Remote Similarity NPC60765
0.5833 Remote Similarity NPC474823
0.5833 Remote Similarity NPC125578
0.5833 Remote Similarity NPC146376
0.5833 Remote Similarity NPC263382
0.5824 Remote Similarity NPC470147
0.5824 Remote Similarity NPC133226
0.5823 Remote Similarity NPC133600
0.5823 Remote Similarity NPC474267
0.5802 Remote Similarity NPC210303
0.5802 Remote Similarity NPC217940
0.5802 Remote Similarity NPC44343
0.5802 Remote Similarity NPC155849
0.5802 Remote Similarity NPC179087
0.58 Remote Similarity NPC471698
0.5795 Remote Similarity NPC285840
0.5795 Remote Similarity NPC327041
0.5789 Remote Similarity NPC478120
0.5789 Remote Similarity NPC472009
0.5789 Remote Similarity NPC61527
0.5783 Remote Similarity NPC284447
0.5783 Remote Similarity NPC124586
0.5783 Remote Similarity NPC16119
0.5783 Remote Similarity NPC248125
0.5773 Remote Similarity NPC280833
0.5765 Remote Similarity NPC101622
0.5765 Remote Similarity NPC151481
0.5765 Remote Similarity NPC94488
0.5761 Remote Similarity NPC474894
0.5761 Remote Similarity NPC112868
0.5755 Remote Similarity NPC469852
0.5753 Remote Similarity NPC234084
0.575 Remote Similarity NPC45097
0.5747 Remote Similarity NPC222244
0.5747 Remote Similarity NPC16349
0.5745 Remote Similarity NPC474359
0.5743 Remote Similarity NPC255410
0.5733 Remote Similarity NPC191643
0.5732 Remote Similarity NPC474400
0.5732 Remote Similarity NPC34622
0.573 Remote Similarity NPC469880
0.573 Remote Similarity NPC188860
0.573 Remote Similarity NPC477202
0.5729 Remote Similarity NPC472007
0.5714 Remote Similarity NPC203335
0.5714 Remote Similarity NPC139712
0.5714 Remote Similarity NPC224270
0.5714 Remote Similarity NPC243272
0.5714 Remote Similarity NPC471569
0.5714 Remote Similarity NPC473947
0.5699 Remote Similarity NPC329829
0.5699 Remote Similarity NPC473712
0.5699 Remote Similarity NPC475159
0.5699 Remote Similarity NPC145914
0.5699 Remote Similarity NPC131002
0.5699 Remote Similarity NPC73310
0.5699 Remote Similarity NPC11332
0.5699 Remote Similarity NPC473780
0.5699 Remote Similarity NPC65930
0.5699 Remote Similarity NPC94875
0.5699 Remote Similarity NPC473529
0.5699 Remote Similarity NPC180363
0.5698 Remote Similarity NPC291062
0.5698 Remote Similarity NPC59558
0.5698 Remote Similarity NPC476037
0.5698 Remote Similarity NPC4299
0.5698 Remote Similarity NPC476012
0.5698 Remote Similarity NPC94743
0.5686 Remote Similarity NPC120299
0.5684 Remote Similarity NPC130030
0.5684 Remote Similarity NPC474424
0.5684 Remote Similarity NPC471494
0.5684 Remote Similarity NPC77971
0.5684 Remote Similarity NPC182383
0.5682 Remote Similarity NPC315843
0.5679 Remote Similarity NPC217537
0.5673 Remote Similarity NPC469851
0.567 Remote Similarity NPC472008
0.567 Remote Similarity NPC472302
0.567 Remote Similarity NPC471956
0.567 Remote Similarity NPC26078
0.567 Remote Similarity NPC473658
0.567 Remote Similarity NPC233997
0.5667 Remote Similarity NPC477203
0.5667 Remote Similarity NPC68156
0.5667 Remote Similarity NPC233071
0.5663 Remote Similarity NPC96414

  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 NPC261732 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
0.6395 Remote Similarity NPD4756 Discovery
0.5854 Remote Similarity NPD2685 Clinical (unspecified phase)
0.5783 Remote Similarity NPD3704 Approved
0.5783 Remote Similarity NPD6108 Clinical (unspecified phase)
0.5625 Remote Similarity NPD6422 Discontinued
0.5618 Remote Similarity NPD8039 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