Structure

Physi-Chem Properties

Molecular Weight:  182.13
Volume:  196.643
LogP:  3.145
LogD:  3.095
LogS:  -3.878
# Rotatable Bonds:  0
TPSA:  26.3
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.538
Synthetic Accessibility Score:  3.612
Fsp3:  0.909
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.619
MDCK Permeability:  2.56E-05
Pgp-inhibitor:  0.371
Pgp-substrate:  0
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.005
30% Bioavailability (F30%):  0.206

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.842
Plasma Protein Binding (PPB):  77.34%
Volume Distribution (VD):  0.681
Pgp-substrate:  50.61%

ADMET: Metabolism

CYP1A2-inhibitor:  0.066
CYP1A2-substrate:  0.375
CYP2C19-inhibitor:  0.185
CYP2C19-substrate:  0.879
CYP2C9-inhibitor:  0.137
CYP2C9-substrate:  0.328
CYP2D6-inhibitor:  0.007
CYP2D6-substrate:  0.539
CYP3A4-inhibitor:  0.065
CYP3A4-substrate:  0.285

ADMET: Excretion

Clearance (CL):  11.065
Half-life (T1/2):  0.435

ADMET: Toxicity

hERG Blockers:  0.01
Human Hepatotoxicity (H-HT):  0.119
Drug-inuced Liver Injury (DILI):  0.09
AMES Toxicity:  0.012
Rat Oral Acute Toxicity:  0.045
Maximum Recommended Daily Dose:  0.18
Skin Sensitization:  0.618
Carcinogencity:  0.204
Eye Corrosion:  0.954
Eye Irritation:  0.898
Respiratory Toxicity:  0.857

Download Data

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

  Natural Product: NPC478126

Natural Product ID:  NPC478126
Common Name*:   2(3H)-Benzofuranone, hexahydro-4,4,7a-trimethyl-
IUPAC Name:   4,4,7a-trimethyl-3a,5,6,7-tetrahydro-3H-1-benzofuran-2-one
Synonyms:  
Standard InCHIKey:  IGSYVKHPYSDDQD-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C11H18O2/c1-10(2)5-4-6-11(3)8(10)7-9(12)13-11/h8H,4-7H2,1-3H3
SMILES:  CC1(CCCC2(C1CC(=O)O2)C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   536454
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000301] Benzofurans

*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
NPO8589 Triticum aestivum Species Poaceae Eukaryota n.a. n.a. n.a. PMID[10993146]
NPO8589 Triticum aestivum Species Poaceae Eukaryota n.a. Tsukuba, Japan 1998-JUN PMID[12381108]
NPO8589 Triticum aestivum Species Poaceae Eukaryota n.a. leaf n.a. PMID[24197199]
NPO8589 Triticum aestivum Species Poaceae Eukaryota n.a. n.a. n.a. PMID[24254087]
NPO8589 Triticum aestivum Species Poaceae Eukaryota n.a. n.a. PMID[31861466]
NPO8589 Triticum aestivum Species Poaceae Eukaryota Root n.a. n.a. Database[FooDB]
NPO8589 Triticum aestivum Species Poaceae Eukaryota Seed n.a. n.a. Database[FooDB]
NPO8589 Triticum aestivum Species Poaceae Eukaryota Shoot n.a. n.a. Database[FooDB]
NPO8589 Triticum aestivum Species Poaceae Eukaryota n.a. n.a. Database[FooDB]
NPO8589 Triticum aestivum Species Poaceae Eukaryota Oil n.a. n.a. Database[FooDB]
NPO8589 Triticum aestivum Species Poaceae Eukaryota Plant n.a. n.a. Database[FooDB]
NPO8589 Triticum aestivum Species Poaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8589 Triticum aestivum Species Poaceae Eukaryota n.a. n.a. Database[Phenol-Explorer]
NPO8589 Triticum aestivum Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8589 Triticum aestivum Species Poaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO8589 Triticum aestivum Species Poaceae 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
NPT119 Organism Triticum aestivum Triticum aestivum GI = 0 % PMID[12381108]
NPT119 Organism Triticum aestivum Triticum aestivum Inhibition = 0 % PMID[12381108]

☑ 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 NPC478126 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
0.918 High Similarity NPC84562
0.8525 High Similarity NPC306750
0.8358 Intermediate Similarity NPC109510
0.8235 Intermediate Similarity NPC55508
0.8154 Intermediate Similarity NPC469868
0.8088 Intermediate Similarity NPC474755
0.7941 Intermediate Similarity NPC197701
0.7887 Intermediate Similarity NPC307865
0.7879 Intermediate Similarity NPC41542
0.7846 Intermediate Similarity NPC19311
0.7846 Intermediate Similarity NPC230047
0.7746 Intermediate Similarity NPC92489
0.7671 Intermediate Similarity NPC73013
0.7647 Intermediate Similarity NPC196197
0.7647 Intermediate Similarity NPC295788
0.7639 Intermediate Similarity NPC143250
0.7586 Intermediate Similarity NPC305182
0.7568 Intermediate Similarity NPC125366
0.7568 Intermediate Similarity NPC134227
0.75 Intermediate Similarity NPC471046
0.7467 Intermediate Similarity NPC48756
0.7467 Intermediate Similarity NPC58631
0.7467 Intermediate Similarity NPC280781
0.7465 Intermediate Similarity NPC96759
0.7432 Intermediate Similarity NPC474754
0.7368 Intermediate Similarity NPC258153
0.7368 Intermediate Similarity NPC476458
0.7368 Intermediate Similarity NPC13494
0.7361 Intermediate Similarity NPC155441
0.7313 Intermediate Similarity NPC157518
0.7246 Intermediate Similarity NPC119838
0.7237 Intermediate Similarity NPC475743
0.7237 Intermediate Similarity NPC38642
0.7237 Intermediate Similarity NPC475665
0.7237 Intermediate Similarity NPC475951
0.7237 Intermediate Similarity NPC209318
0.7237 Intermediate Similarity NPC223330
0.7231 Intermediate Similarity NPC204173
0.7231 Intermediate Similarity NPC84218
0.72 Intermediate Similarity NPC118987
0.7183 Intermediate Similarity NPC478227
0.7179 Intermediate Similarity NPC291310
0.7179 Intermediate Similarity NPC65133
0.7179 Intermediate Similarity NPC79308
0.7167 Intermediate Similarity NPC274261
0.7167 Intermediate Similarity NPC291724
0.7162 Intermediate Similarity NPC471151
0.7143 Intermediate Similarity NPC226988
0.7143 Intermediate Similarity NPC178541
0.7105 Intermediate Similarity NPC60568
0.7105 Intermediate Similarity NPC170038
0.7089 Intermediate Similarity NPC477445
0.7083 Intermediate Similarity NPC475230
0.7083 Intermediate Similarity NPC248567
0.7067 Intermediate Similarity NPC35574
0.7059 Intermediate Similarity NPC474768
0.7059 Intermediate Similarity NPC469791
0.7051 Intermediate Similarity NPC194637
0.7051 Intermediate Similarity NPC15091
0.7027 Intermediate Similarity NPC476601
0.7027 Intermediate Similarity NPC41017
0.7013 Intermediate Similarity NPC271572
0.7013 Intermediate Similarity NPC474870
0.7013 Intermediate Similarity NPC472230
0.7013 Intermediate Similarity NPC232625
0.7013 Intermediate Similarity NPC472229
0.7 Intermediate Similarity NPC9231
0.6962 Remote Similarity NPC473299
0.6962 Remote Similarity NPC139566
0.6962 Remote Similarity NPC470011
0.6962 Remote Similarity NPC219011
0.6962 Remote Similarity NPC477434
0.6962 Remote Similarity NPC97505
0.6957 Remote Similarity NPC42060
0.6957 Remote Similarity NPC477931
0.6957 Remote Similarity NPC268736
0.6944 Remote Similarity NPC469940
0.6933 Remote Similarity NPC474404
0.6912 Remote Similarity NPC128608
0.6897 Remote Similarity NPC282440
0.6892 Remote Similarity NPC72444
0.6892 Remote Similarity NPC179858
0.6892 Remote Similarity NPC212733
0.6892 Remote Similarity NPC39362
0.6885 Remote Similarity NPC314084
0.6883 Remote Similarity NPC1882
0.6883 Remote Similarity NPC261616
0.6875 Remote Similarity NPC52628
0.6875 Remote Similarity NPC62572
0.6866 Remote Similarity NPC83088
0.6857 Remote Similarity NPC476928
0.6857 Remote Similarity NPC130459
0.6857 Remote Similarity NPC263161
0.6857 Remote Similarity NPC474221
0.6857 Remote Similarity NPC478180
0.6842 Remote Similarity NPC31031
0.6842 Remote Similarity NPC243594
0.6835 Remote Similarity NPC470948
0.6829 Remote Similarity NPC471221
0.6829 Remote Similarity NPC221993
0.6825 Remote Similarity NPC319589
0.6812 Remote Similarity NPC215987
0.6812 Remote Similarity NPC295256
0.6812 Remote Similarity NPC306805
0.6806 Remote Similarity NPC108131
0.6806 Remote Similarity NPC477929
0.68 Remote Similarity NPC104806
0.68 Remote Similarity NPC4209
0.6795 Remote Similarity NPC20096
0.6795 Remote Similarity NPC50658
0.6795 Remote Similarity NPC48673
0.679 Remote Similarity NPC477441
0.679 Remote Similarity NPC6979
0.679 Remote Similarity NPC85698
0.679 Remote Similarity NPC477920
0.6761 Remote Similarity NPC469724
0.6761 Remote Similarity NPC31187
0.6761 Remote Similarity NPC470956
0.6761 Remote Similarity NPC475977
0.6761 Remote Similarity NPC281203
0.6761 Remote Similarity NPC100917
0.6757 Remote Similarity NPC167702
0.6757 Remote Similarity NPC280026
0.6753 Remote Similarity NPC201276
0.6753 Remote Similarity NPC80891
0.6753 Remote Similarity NPC263951
0.6747 Remote Similarity NPC472234
0.6747 Remote Similarity NPC472233
0.6747 Remote Similarity NPC173042
0.6716 Remote Similarity NPC66145
0.6712 Remote Similarity NPC89310
0.6712 Remote Similarity NPC472309
0.6712 Remote Similarity NPC470243
0.6711 Remote Similarity NPC207010
0.6711 Remote Similarity NPC317913
0.6711 Remote Similarity NPC477918
0.6711 Remote Similarity NPC298168
0.6711 Remote Similarity NPC143133
0.6709 Remote Similarity NPC102156
0.6709 Remote Similarity NPC148740
0.6709 Remote Similarity NPC289486
0.6709 Remote Similarity NPC476935
0.6709 Remote Similarity NPC242771
0.6709 Remote Similarity NPC100366
0.6709 Remote Similarity NPC164289
0.6709 Remote Similarity NPC61107
0.6709 Remote Similarity NPC311642
0.6707 Remote Similarity NPC470012
0.6707 Remote Similarity NPC181103
0.6707 Remote Similarity NPC175293
0.6707 Remote Similarity NPC305029
0.6667 Remote Similarity NPC474962
0.6667 Remote Similarity NPC252032
0.6667 Remote Similarity NPC469941
0.6667 Remote Similarity NPC185529
0.6667 Remote Similarity NPC478111
0.6667 Remote Similarity NPC195424
0.6667 Remote Similarity NPC64466
0.6667 Remote Similarity NPC473350
0.6667 Remote Similarity NPC13105
0.6667 Remote Similarity NPC476734
0.6667 Remote Similarity NPC472146
0.6667 Remote Similarity NPC319671
0.6667 Remote Similarity NPC76286
0.6667 Remote Similarity NPC472853
0.6667 Remote Similarity NPC477934
0.6627 Remote Similarity NPC476435
0.6627 Remote Similarity NPC474845
0.6627 Remote Similarity NPC477128
0.6627 Remote Similarity NPC215831
0.6625 Remote Similarity NPC476721
0.6625 Remote Similarity NPC472847
0.6625 Remote Similarity NPC471037
0.6623 Remote Similarity NPC171426
0.6623 Remote Similarity NPC475725
0.6623 Remote Similarity NPC476732
0.6623 Remote Similarity NPC472608
0.6623 Remote Similarity NPC199965
0.6623 Remote Similarity NPC34046
0.6623 Remote Similarity NPC224802
0.6623 Remote Similarity NPC80089
0.6623 Remote Similarity NPC324700
0.6622 Remote Similarity NPC279241
0.6622 Remote Similarity NPC474123
0.662 Remote Similarity NPC329466
0.662 Remote Similarity NPC328304
0.662 Remote Similarity NPC472984
0.6618 Remote Similarity NPC253204
0.661 Remote Similarity NPC52700
0.661 Remote Similarity NPC105329
0.661 Remote Similarity NPC145045
0.661 Remote Similarity NPC63182
0.661 Remote Similarity NPC314679
0.6588 Remote Similarity NPC49420
0.6588 Remote Similarity NPC474065
0.6588 Remote Similarity NPC216137
0.6588 Remote Similarity NPC252433
0.6585 Remote Similarity NPC476717
0.6585 Remote Similarity NPC250981
0.6585 Remote Similarity NPC471042

  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 NPC478126 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
0.7246 Intermediate Similarity NPD229 Approved
0.7206 Intermediate Similarity NPD4224 Phase 2
0.7183 Intermediate Similarity NPD5777 Approved
0.7123 Intermediate Similarity NPD3702 Approved
0.7097 Intermediate Similarity NPD615 Clinical (unspecified phase)
0.6964 Remote Similarity NPD387 Clinical (unspecified phase)
0.6812 Remote Similarity NPD9496 Clinical (unspecified phase)
0.68 Remote Similarity NPD6117 Approved
0.6761 Remote Similarity NPD5361 Clinical (unspecified phase)
0.6761 Remote Similarity NPD5360 Phase 3
0.6757 Remote Similarity NPD6113 Clinical (unspecified phase)
0.6712 Remote Similarity NPD6081 Approved
0.6711 Remote Similarity NPD6116 Phase 1
0.6623 Remote Similarity NPD6114 Approved
0.6623 Remote Similarity NPD6115 Approved
0.6623 Remote Similarity NPD6697 Approved
0.6623 Remote Similarity NPD6118 Approved
0.661 Remote Similarity NPD634 Phase 3
0.6582 Remote Similarity NPD1780 Approved
0.6582 Remote Similarity NPD1779 Approved
0.6571 Remote Similarity NPD3171 Clinical (unspecified phase)
0.6486 Remote Similarity NPD4758 Discontinued
0.6463 Remote Similarity NPD1694 Approved
0.6438 Remote Similarity NPD3700 Clinical (unspecified phase)
0.6438 Remote Similarity NPD3699 Clinical (unspecified phase)
0.6437 Remote Similarity NPD6001 Approved
0.6364 Remote Similarity NPD6356 Clinical (unspecified phase)
0.631 Remote Similarity NPD3573 Approved
0.6279 Remote Similarity NPD5207 Approved
0.6267 Remote Similarity NPD4809 Clinical (unspecified phase)
0.6267 Remote Similarity NPD4808 Clinical (unspecified phase)
0.6234 Remote Similarity NPD3703 Phase 2
0.6216 Remote Similarity NPD3698 Phase 2
0.6216 Remote Similarity NPD3725 Approved
0.6216 Remote Similarity NPD3726 Approved
0.6207 Remote Similarity NPD8035 Phase 2
0.6207 Remote Similarity NPD8034 Phase 2
0.619 Remote Similarity NPD6098 Approved
0.6133 Remote Similarity NPD4245 Approved
0.6133 Remote Similarity NPD4789 Approved
0.6133 Remote Similarity NPD4244 Approved
0.6098 Remote Similarity NPD4752 Clinical (unspecified phase)
0.6087 Remote Similarity NPD3198 Approved
0.6071 Remote Similarity NPD9449 Clinical (unspecified phase)
0.6071 Remote Similarity NPD7520 Clinical (unspecified phase)
0.6061 Remote Similarity NPD3729 Clinical (unspecified phase)
0.6047 Remote Similarity NPD5208 Approved
0.6022 Remote Similarity NPD1700 Approved
0.6 Remote Similarity NPD5330 Approved
0.6 Remote Similarity NPD3186 Phase 1
0.6 Remote Similarity NPD5364 Discontinued
0.6 Remote Similarity NPD6409 Approved
0.6 Remote Similarity NPD7334 Approved
0.6 Remote Similarity NPD7146 Approved
0.6 Remote Similarity NPD6684 Approved
0.6 Remote Similarity NPD7521 Approved
0.5977 Remote Similarity NPD6080 Approved
0.5977 Remote Similarity NPD6904 Approved
0.5977 Remote Similarity NPD6673 Approved
0.5909 Remote Similarity NPD5692 Phase 3
0.5902 Remote Similarity NPD2699 Approved
0.5889 Remote Similarity NPD7901 Clinical (unspecified phase)
0.5889 Remote Similarity NPD7900 Approved
0.5873 Remote Similarity NPD2266 Phase 2
0.5862 Remote Similarity NPD6672 Approved
0.5862 Remote Similarity NPD5737 Approved
0.5862 Remote Similarity NPD7513 Clinical (unspecified phase)
0.5862 Remote Similarity NPD6903 Approved
0.5843 Remote Similarity NPD6050 Approved
0.5843 Remote Similarity NPD5693 Phase 1
0.5843 Remote Similarity NPD5694 Approved
0.5833 Remote Similarity NPD3670 Clinical (unspecified phase)
0.5833 Remote Similarity NPD3669 Approved
0.5814 Remote Similarity NPD3574 Clinical (unspecified phase)
0.5811 Remote Similarity NPD375 Phase 2
0.5802 Remote Similarity NPD4802 Phase 2
0.5802 Remote Similarity NPD3671 Phase 1
0.5802 Remote Similarity NPD4238 Approved
0.5778 Remote Similarity NPD6399 Phase 3
0.5775 Remote Similarity NPD9656 Approved
0.5773 Remote Similarity NPD6008 Approved
0.5738 Remote Similarity NPD367 Approved
0.5714 Remote Similarity NPD343 Approved
0.5714 Remote Similarity NPD345 Approved
0.5714 Remote Similarity NPD9447 Approved
0.5714 Remote Similarity NPD344 Approved
0.5714 Remote Similarity NPD7748 Approved
0.5699 Remote Similarity NPD7902 Approved
0.569 Remote Similarity NPD3206 Approved
0.5667 Remote Similarity NPD5284 Approved
0.5667 Remote Similarity NPD5281 Approved
0.5652 Remote Similarity NPD5654 Approved
0.5652 Remote Similarity NPD5695 Phase 3
0.5638 Remote Similarity NPD5696 Approved
0.5632 Remote Similarity NPD3618 Phase 1
0.5625 Remote Similarity NPD2257 Approved
0.561 Remote Similarity NPD3617 Approved
0.5606 Remote Similarity NPD9638 Phase 2

  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