Structure

Physi-Chem Properties

Molecular Weight:  156.08
Volume:  153.546
LogP:  -0.185
LogD:  -0.403
LogS:  -0.9
# Rotatable Bonds:  0
TPSA:  49.69
# H-Bond Aceptor:  3
# H-Bond Donor:  2
# Rings:  2
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.479
Synthetic Accessibility Score:  4.618
Fsp3:  0.75
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:  -4.639
MDCK Permeability:  3.35351905960124e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.015
Human Intestinal Absorption (HIA):  0.091
20% Bioavailability (F20%):  0.043
30% Bioavailability (F30%):  0.043

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.995
Plasma Protein Binding (PPB):  13.36397933959961%
Volume Distribution (VD):  1.8
Pgp-substrate:  81.9664535522461%

ADMET: Metabolism

CYP1A2-inhibitor:  0.015
CYP1A2-substrate:  0.44
CYP2C19-inhibitor:  0.019
CYP2C19-substrate:  0.569
CYP2C9-inhibitor:  0.004
CYP2C9-substrate:  0.302
CYP2D6-inhibitor:  0.003
CYP2D6-substrate:  0.186
CYP3A4-inhibitor:  0.013
CYP3A4-substrate:  0.141

ADMET: Excretion

Clearance (CL):  3.342
Half-life (T1/2):  0.712

ADMET: Toxicity

hERG Blockers:  0.019
Human Hepatotoxicity (H-HT):  0.14
Drug-inuced Liver Injury (DILI):  0.032
AMES Toxicity:  0.305
Rat Oral Acute Toxicity:  0.535
Maximum Recommended Daily Dose:  0.387
Skin Sensitization:  0.53
Carcinogencity:  0.232
Eye Corrosion:  0.041
Eye Irritation:  0.956
Respiratory Toxicity:  0.138

Download Data

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

  Natural Product: NPC473722

Natural Product ID:  NPC473722
Common Name*:   (3Ar,7Ar)-2,3,3A,6,7,7A-Hexahydrobenzofuran-3A,6-Diol
IUPAC Name:   (3aR,7aR)-3,6,7,7a-tetrahydro-2H-1-benzofuran-3a,6-diol
Synonyms:  
Standard InCHIKey:  SWUWGVKRMOEGEN-VVXQKDJTSA-N
Standard InCHI:  InChI=1S/C8H12O3/c9-6-1-2-8(10)3-4-11-7(8)5-6/h1-2,6-7,9-10H,3-5H2/t6?,7-,8+/m1/s1
SMILES:  C1COC2C1(C=CC(C2)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL450316
PubChem CID:   44567078
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
NPO33459 cornus controversa Species Cornaceae Eukaryota n.a. n.a. n.a. PMID[3236014]

☑ 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
NPT168 Cell Line P388 Mus musculus IC50 = 40.8 ug.mL-1 PMID[573725]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 > 100.0 ug.mL-1 PMID[573725]

☑ 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 NPC473722 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
0.8551 High Similarity NPC474280
0.8194 Intermediate Similarity NPC474278
0.7973 Intermediate Similarity NPC475210
0.7857 Intermediate Similarity NPC129630
0.7846 Intermediate Similarity NPC258788
0.7808 Intermediate Similarity NPC474197
0.7794 Intermediate Similarity NPC267027
0.7662 Intermediate Similarity NPC474252
0.76 Intermediate Similarity NPC68119
0.76 Intermediate Similarity NPC13823
0.7541 Intermediate Similarity NPC200772
0.7467 Intermediate Similarity NPC476703
0.7429 Intermediate Similarity NPC82337
0.7391 Intermediate Similarity NPC250836
0.7344 Intermediate Similarity NPC227135
0.7333 Intermediate Similarity NPC170148
0.7324 Intermediate Similarity NPC272961
0.7297 Intermediate Similarity NPC24590
0.7297 Intermediate Similarity NPC190859
0.7286 Intermediate Similarity NPC326310
0.7273 Intermediate Similarity NPC476701
0.7273 Intermediate Similarity NPC226848
0.7273 Intermediate Similarity NPC291260
0.7222 Intermediate Similarity NPC472947
0.7206 Intermediate Similarity NPC321867
0.7206 Intermediate Similarity NPC68679
0.7206 Intermediate Similarity NPC207007
0.7162 Intermediate Similarity NPC476709
0.716 Intermediate Similarity NPC298595
0.7143 Intermediate Similarity NPC181838
0.7143 Intermediate Similarity NPC137345
0.7105 Intermediate Similarity NPC236228
0.7105 Intermediate Similarity NPC256720
0.7089 Intermediate Similarity NPC246621
0.7073 Intermediate Similarity NPC281316
0.7067 Intermediate Similarity NPC471525
0.7059 Intermediate Similarity NPC99487
0.7059 Intermediate Similarity NPC469694
0.7059 Intermediate Similarity NPC66020
0.7042 Intermediate Similarity NPC311736
0.7037 Intermediate Similarity NPC32676
0.7013 Intermediate Similarity NPC40049
0.7 Intermediate Similarity NPC475221
0.7 Intermediate Similarity NPC477390
0.7 Intermediate Similarity NPC300593
0.7 Intermediate Similarity NPC477385
0.6986 Remote Similarity NPC473893
0.6986 Remote Similarity NPC74722
0.6986 Remote Similarity NPC239373
0.6986 Remote Similarity NPC304690
0.6986 Remote Similarity NPC16964
0.6986 Remote Similarity NPC329989
0.697 Remote Similarity NPC48891
0.6944 Remote Similarity NPC73603
0.6944 Remote Similarity NPC163290
0.6944 Remote Similarity NPC59442
0.6923 Remote Similarity NPC477089
0.6912 Remote Similarity NPC475931
0.6912 Remote Similarity NPC122239
0.6905 Remote Similarity NPC228415
0.6905 Remote Similarity NPC87189
0.6901 Remote Similarity NPC471200
0.6883 Remote Similarity NPC229655
0.6867 Remote Similarity NPC478112
0.6867 Remote Similarity NPC255143
0.6867 Remote Similarity NPC278283
0.6866 Remote Similarity NPC52012
0.6849 Remote Similarity NPC305698
0.6842 Remote Similarity NPC144995
0.6842 Remote Similarity NPC227814
0.6842 Remote Similarity NPC477422
0.6824 Remote Similarity NPC49783
0.6824 Remote Similarity NPC478110
0.6818 Remote Similarity NPC148216
0.6818 Remote Similarity NPC232247
0.6818 Remote Similarity NPC130209
0.6818 Remote Similarity NPC148163
0.6818 Remote Similarity NPC251666
0.6812 Remote Similarity NPC240506
0.6795 Remote Similarity NPC477426
0.6795 Remote Similarity NPC477427
0.6795 Remote Similarity NPC474826
0.6795 Remote Similarity NPC477425
0.6786 Remote Similarity NPC23622
0.6769 Remote Similarity NPC474496
0.6765 Remote Similarity NPC41180
0.6765 Remote Similarity NPC181872
0.6765 Remote Similarity NPC152438
0.6765 Remote Similarity NPC155025
0.6753 Remote Similarity NPC12696
0.675 Remote Similarity NPC474592
0.675 Remote Similarity NPC236707
0.6714 Remote Similarity NPC475251
0.6712 Remote Similarity NPC25298
0.6712 Remote Similarity NPC259299
0.6712 Remote Similarity NPC473357
0.6712 Remote Similarity NPC193029
0.6711 Remote Similarity NPC265485
0.6711 Remote Similarity NPC220939
0.6711 Remote Similarity NPC132938
0.6709 Remote Similarity NPC326753
0.6709 Remote Similarity NPC475980
0.6709 Remote Similarity NPC470944
0.6707 Remote Similarity NPC44261
0.6707 Remote Similarity NPC474809
0.6706 Remote Similarity NPC231784
0.6667 Remote Similarity NPC311163
0.6667 Remote Similarity NPC477389
0.6667 Remote Similarity NPC472379
0.6667 Remote Similarity NPC474894
0.6667 Remote Similarity NPC308844
0.6667 Remote Similarity NPC477387
0.6667 Remote Similarity NPC471270
0.6667 Remote Similarity NPC107848
0.6667 Remote Similarity NPC230623
0.6667 Remote Similarity NPC287339
0.6667 Remote Similarity NPC329626
0.6628 Remote Similarity NPC133450
0.6628 Remote Similarity NPC115607
0.6628 Remote Similarity NPC299527
0.6627 Remote Similarity NPC220167
0.6627 Remote Similarity NPC136699
0.6627 Remote Similarity NPC83702
0.6625 Remote Similarity NPC233295
0.6625 Remote Similarity NPC471537
0.6622 Remote Similarity NPC471238
0.6622 Remote Similarity NPC224532
0.662 Remote Similarity NPC473508
0.662 Remote Similarity NPC83200
0.6615 Remote Similarity NPC35756
0.6588 Remote Similarity NPC477386
0.6588 Remote Similarity NPC477388
0.6585 Remote Similarity NPC471408
0.6585 Remote Similarity NPC259858
0.6579 Remote Similarity NPC471268
0.6579 Remote Similarity NPC306085
0.6579 Remote Similarity NPC471272
0.6579 Remote Similarity NPC23954
0.6579 Remote Similarity NPC471271
0.6575 Remote Similarity NPC37382
0.6575 Remote Similarity NPC202017
0.6575 Remote Similarity NPC276299
0.6567 Remote Similarity NPC281590
0.6556 Remote Similarity NPC210717
0.6556 Remote Similarity NPC103165
0.6552 Remote Similarity NPC197107
0.6552 Remote Similarity NPC15059
0.6552 Remote Similarity NPC177668
0.6548 Remote Similarity NPC471494
0.6548 Remote Similarity NPC470658
0.6543 Remote Similarity NPC95124
0.6543 Remote Similarity NPC162741
0.6543 Remote Similarity NPC471266
0.6543 Remote Similarity NPC206062
0.6543 Remote Similarity NPC91332
0.6533 Remote Similarity NPC471560
0.6533 Remote Similarity NPC130618
0.6528 Remote Similarity NPC110241
0.6512 Remote Similarity NPC119740
0.6512 Remote Similarity NPC309656
0.6512 Remote Similarity NPC150063
0.6506 Remote Similarity NPC477786
0.6506 Remote Similarity NPC477784
0.6506 Remote Similarity NPC477785
0.6506 Remote Similarity NPC185605
0.65 Remote Similarity NPC248775
0.65 Remote Similarity NPC267231
0.65 Remote Similarity NPC231739
0.65 Remote Similarity NPC11796
0.65 Remote Similarity NPC3852
0.65 Remote Similarity NPC167891
0.65 Remote Similarity NPC83351
0.65 Remote Similarity NPC218817
0.65 Remote Similarity NPC475699
0.6494 Remote Similarity NPC470435
0.6486 Remote Similarity NPC114651
0.6484 Remote Similarity NPC261807
0.6484 Remote Similarity NPC120446
0.6479 Remote Similarity NPC64971
0.6477 Remote Similarity NPC475441
0.6477 Remote Similarity NPC208839
0.6471 Remote Similarity NPC469910
0.6471 Remote Similarity NPC247826
0.6463 Remote Similarity NPC24417
0.6463 Remote Similarity NPC475944
0.6463 Remote Similarity NPC52861
0.6456 Remote Similarity NPC293223
0.6447 Remote Similarity NPC189745
0.6447 Remote Similarity NPC4299
0.6444 Remote Similarity NPC8774
0.6438 Remote Similarity NPC19769
0.6438 Remote Similarity NPC470123
0.6437 Remote Similarity NPC97103
0.6429 Remote Similarity NPC186155
0.6429 Remote Similarity NPC160517
0.6429 Remote Similarity NPC295799
0.6429 Remote Similarity NPC473866
0.6429 Remote Similarity NPC78673
0.642 Remote Similarity NPC86971
0.642 Remote Similarity NPC473980

  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 NPC473722 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
0.7206 Intermediate Similarity NPD368 Approved
0.6818 Remote Similarity NPD342 Phase 1
0.6543 Remote Similarity NPD5790 Clinical (unspecified phase)
0.6522 Remote Similarity NPD585 Clinical (unspecified phase)
0.6494 Remote Similarity NPD4732 Discontinued
0.6395 Remote Similarity NPD7524 Approved
0.6341 Remote Similarity NPD4819 Approved
0.6341 Remote Similarity NPD4820 Approved
0.6341 Remote Similarity NPD4822 Approved
0.6341 Remote Similarity NPD4821 Approved
0.6296 Remote Similarity NPD4268 Approved
0.6296 Remote Similarity NPD4271 Approved
0.6279 Remote Similarity NPD4249 Approved
0.6235 Remote Similarity NPD7338 Clinical (unspecified phase)
0.6207 Remote Similarity NPD4250 Approved
0.6207 Remote Similarity NPD4251 Approved
0.6145 Remote Similarity NPD7514 Phase 3
0.6145 Remote Similarity NPD7332 Phase 2
0.6125 Remote Similarity NPD8264 Approved
0.6118 Remote Similarity NPD6695 Phase 3
0.6118 Remote Similarity NPD7154 Phase 3
0.6111 Remote Similarity NPD7983 Approved
0.6098 Remote Similarity NPD7322 Clinical (unspecified phase)
0.6049 Remote Similarity NPD6933 Approved
0.6 Remote Similarity NPD6698 Approved
0.6 Remote Similarity NPD46 Approved
0.6 Remote Similarity NPD7838 Discovery
0.5952 Remote Similarity NPD6931 Approved
0.5952 Remote Similarity NPD6930 Phase 2
0.5938 Remote Similarity NPD5344 Discontinued
0.5904 Remote Similarity NPD7145 Approved
0.5895 Remote Similarity NPD4225 Approved
0.5882 Remote Similarity NPD6902 Approved
0.5862 Remote Similarity NPD6400 Clinical (unspecified phase)
0.5851 Remote Similarity NPD4792 Clinical (unspecified phase)
0.5843 Remote Similarity NPD7750 Discontinued
0.5833 Remote Similarity NPD6929 Approved
0.5802 Remote Similarity NPD6924 Approved
0.5802 Remote Similarity NPD6926 Approved
0.5783 Remote Similarity NPD5776 Phase 2
0.5783 Remote Similarity NPD6932 Approved
0.5783 Remote Similarity NPD6925 Approved
0.5775 Remote Similarity NPD4219 Approved
0.5747 Remote Similarity NPD5362 Discontinued
0.5747 Remote Similarity NPD6110 Phase 1
0.5729 Remote Similarity NPD8029 Clinical (unspecified phase)
0.5728 Remote Similarity NPD8413 Clinical (unspecified phase)
0.5699 Remote Similarity NPD5779 Approved
0.5699 Remote Similarity NPD5778 Approved
0.5698 Remote Similarity NPD4790 Discontinued
0.5698 Remote Similarity NPD6898 Phase 1
0.5692 Remote Similarity NPD4265 Approved
0.5676 Remote Similarity NPD1145 Discontinued
0.5676 Remote Similarity NPD4246 Clinical (unspecified phase)
0.5672 Remote Similarity NPD9410 Clinical (unspecified phase)
0.5667 Remote Similarity NPD4751 Clinical (unspecified phase)
0.5663 Remote Similarity NPD3701 Clinical (unspecified phase)
0.5632 Remote Similarity NPD4270 Approved
0.5632 Remote Similarity NPD4269 Approved
0.5632 Remote Similarity NPD6435 Approved
0.5625 Remote Similarity NPD7144 Approved
0.5625 Remote Similarity NPD7143 Approved
0.5618 Remote Similarity NPD6893 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