Structure

Physi-Chem Properties

Molecular Weight:  156.08
Volume:  153.546
LogP:  -0.186
LogD:  -1.009
LogS:  -0.676
# Rotatable Bonds:  0
TPSA:  46.53
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.547
Synthetic Accessibility Score:  4.116
Fsp3:  0.875
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:  -4.563
MDCK Permeability:  1.666043681325391e-05
Pgp-inhibitor:  0.014
Pgp-substrate:  0.227
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.005
30% Bioavailability (F30%):  0.018

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.728
Plasma Protein Binding (PPB):  24.490982055664062%
Volume Distribution (VD):  1.353
Pgp-substrate:  80.88568115234375%

ADMET: Metabolism

CYP1A2-inhibitor:  0.01
CYP1A2-substrate:  0.752
CYP2C19-inhibitor:  0.019
CYP2C19-substrate:  0.393
CYP2C9-inhibitor:  0.007
CYP2C9-substrate:  0.088
CYP2D6-inhibitor:  0.005
CYP2D6-substrate:  0.149
CYP3A4-inhibitor:  0.011
CYP3A4-substrate:  0.187

ADMET: Excretion

Clearance (CL):  5.844
Half-life (T1/2):  0.82

ADMET: Toxicity

hERG Blockers:  0.02
Human Hepatotoxicity (H-HT):  0.292
Drug-inuced Liver Injury (DILI):  0.088
AMES Toxicity:  0.871
Rat Oral Acute Toxicity:  0.34
Maximum Recommended Daily Dose:  0.386
Skin Sensitization:  0.265
Carcinogencity:  0.571
Eye Corrosion:  0.268
Eye Irritation:  0.901
Respiratory Toxicity:  0.217

Download Data

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

  Natural Product: NPC10659

Natural Product ID:  NPC10659
Common Name*:   (3As,7Ar)-3A-Hydroxyhexahydrobenzofuran-6(2H)-One
IUPAC Name:   (3aS,7aR)-3a-hydroxy-2,3,4,5,7,7a-hexahydro-1-benzofuran-6-one
Synonyms:  
Standard InCHIKey:  ZCBQZDMJIVJQLX-SFYZADRCSA-N
Standard InCHI:  InChI=1S/C8H12O3/c9-6-1-2-8(10)3-4-11-7(8)5-6/h7,10H,1-5H2/t7-,8+/m1/s1
SMILES:  O=C1CC[C@]2([C@@H](C1)OCC2)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL463263
PubChem CID:   25199269
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 = 43.0 ug.mL-1 PMID[538408]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 > 100.0 ug.mL-1 PMID[538408]

☑ 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 NPC10659 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
0.7246 Intermediate Similarity NPC469925
0.6892 Remote Similarity NPC125164
0.6714 Remote Similarity NPC469926
0.6711 Remote Similarity NPC474197
0.6707 Remote Similarity NPC475729
0.6707 Remote Similarity NPC476717
0.6707 Remote Similarity NPC474215
0.6706 Remote Similarity NPC230623
0.6667 Remote Similarity NPC235788
0.6585 Remote Similarity NPC51267
0.6579 Remote Similarity NPC68565
0.6579 Remote Similarity NPC35871
0.6543 Remote Similarity NPC227170
0.6533 Remote Similarity NPC475232
0.6533 Remote Similarity NPC473775
0.6533 Remote Similarity NPC475260
0.6533 Remote Similarity NPC473699
0.6533 Remote Similarity NPC51249
0.6533 Remote Similarity NPC474100
0.6471 Remote Similarity NPC469924
0.6463 Remote Similarity NPC291310
0.6463 Remote Similarity NPC115995
0.6438 Remote Similarity NPC82315
0.6418 Remote Similarity NPC293692
0.641 Remote Similarity NPC474003
0.6386 Remote Similarity NPC478111
0.6364 Remote Similarity NPC179922
0.6364 Remote Similarity NPC228411
0.6364 Remote Similarity NPC247877
0.6364 Remote Similarity NPC309127
0.6329 Remote Similarity NPC475725
0.6329 Remote Similarity NPC470014
0.6301 Remote Similarity NPC53879
0.6301 Remote Similarity NPC57788
0.6296 Remote Similarity NPC67254
0.6292 Remote Similarity NPC17336
0.6265 Remote Similarity NPC477434
0.625 Remote Similarity NPC275243
0.6234 Remote Similarity NPC477867
0.6232 Remote Similarity NPC470363
0.6232 Remote Similarity NPC475821
0.619 Remote Similarity NPC46254
0.619 Remote Similarity NPC476715
0.6176 Remote Similarity NPC220922
0.6176 Remote Similarity NPC61567
0.6163 Remote Similarity NPC476435
0.6163 Remote Similarity NPC53158
0.6145 Remote Similarity NPC476721
0.6145 Remote Similarity NPC268578
0.6145 Remote Similarity NPC217559
0.6145 Remote Similarity NPC292458
0.6143 Remote Similarity NPC469921
0.6133 Remote Similarity NPC28526
0.6125 Remote Similarity NPC11796
0.6125 Remote Similarity NPC218817
0.6125 Remote Similarity NPC475616
0.6118 Remote Similarity NPC80700
0.6118 Remote Similarity NPC262026
0.6111 Remote Similarity NPC314103
0.6104 Remote Similarity NPC474755
0.6098 Remote Similarity NPC50658
0.6092 Remote Similarity NPC61688
0.6087 Remote Similarity NPC278008
0.6087 Remote Similarity NPC253995
0.6081 Remote Similarity NPC286842
0.6076 Remote Similarity NPC474020
0.6071 Remote Similarity NPC25037
0.6071 Remote Similarity NPC475689
0.6071 Remote Similarity NPC34984
0.6056 Remote Similarity NPC469923
0.6049 Remote Similarity NPC31302
0.6049 Remote Similarity NPC245029
0.6047 Remote Similarity NPC314364
0.6047 Remote Similarity NPC263802
0.6044 Remote Similarity NPC279722
0.6029 Remote Similarity NPC198377
0.6027 Remote Similarity NPC476330
0.6027 Remote Similarity NPC295256
0.6026 Remote Similarity NPC215030
0.6023 Remote Similarity NPC472146
0.6023 Remote Similarity NPC185529
0.6023 Remote Similarity NPC65359
0.6 Remote Similarity NPC214030
0.6 Remote Similarity NPC68303
0.6 Remote Similarity NPC307126
0.6 Remote Similarity NPC473350
0.6 Remote Similarity NPC83108
0.6 Remote Similarity NPC307865
0.6 Remote Similarity NPC185116
0.5978 Remote Similarity NPC236176
0.5977 Remote Similarity NPC87189
0.5977 Remote Similarity NPC471221
0.5977 Remote Similarity NPC228415
0.5977 Remote Similarity NPC226491
0.5977 Remote Similarity NPC477614
0.5976 Remote Similarity NPC472948
0.5974 Remote Similarity NPC470243
0.5972 Remote Similarity NPC474552
0.597 Remote Similarity NPC53463
0.597 Remote Similarity NPC469937
0.597 Remote Similarity NPC320588
0.597 Remote Similarity NPC23155
0.5968 Remote Similarity NPC282440
0.5968 Remote Similarity NPC133771
0.5957 Remote Similarity NPC305085
0.5957 Remote Similarity NPC84042
0.5955 Remote Similarity NPC216137
0.5955 Remote Similarity NPC469627
0.5952 Remote Similarity NPC472847
0.5949 Remote Similarity NPC81052
0.593 Remote Similarity NPC235196
0.593 Remote Similarity NPC92139
0.593 Remote Similarity NPC228593
0.5926 Remote Similarity NPC191345
0.5926 Remote Similarity NPC252483
0.5926 Remote Similarity NPC478084
0.5921 Remote Similarity NPC98711
0.5909 Remote Similarity NPC253618
0.5909 Remote Similarity NPC77001
0.5909 Remote Similarity NPC477440
0.5909 Remote Similarity NPC477443
0.5904 Remote Similarity NPC211049
0.5904 Remote Similarity NPC116320
0.5904 Remote Similarity NPC119922
0.5902 Remote Similarity NPC76051
0.5895 Remote Similarity NPC471254
0.5882 Remote Similarity NPC79308
0.587 Remote Similarity NPC477264
0.587 Remote Similarity NPC163685
0.5867 Remote Similarity NPC472984
0.5862 Remote Similarity NPC23622
0.5857 Remote Similarity NPC179624
0.5846 Remote Similarity NPC305182
0.5843 Remote Similarity NPC477442
0.5843 Remote Similarity NPC477433
0.5843 Remote Similarity NPC477444
0.5833 Remote Similarity NPC471253
0.5833 Remote Similarity NPC477936
0.5833 Remote Similarity NPC317066
0.5833 Remote Similarity NPC469922
0.5833 Remote Similarity NPC253204
0.5824 Remote Similarity NPC217567
0.5824 Remote Similarity NPC114162
0.5824 Remote Similarity NPC76136
0.5824 Remote Similarity NPC329713
0.5824 Remote Similarity NPC206878
0.5824 Remote Similarity NPC469819
0.5823 Remote Similarity NPC317212
0.5814 Remote Similarity NPC477205
0.5811 Remote Similarity NPC157518
0.5811 Remote Similarity NPC215987
0.5811 Remote Similarity NPC306805
0.5806 Remote Similarity NPC240994
0.5806 Remote Similarity NPC273545
0.5806 Remote Similarity NPC17326
0.5806 Remote Similarity NPC134454
0.5806 Remote Similarity NPC27105
0.5795 Remote Similarity NPC476706
0.5795 Remote Similarity NPC476707
0.5789 Remote Similarity NPC119838
0.5789 Remote Similarity NPC259654
0.5789 Remote Similarity NPC298266
0.5789 Remote Similarity NPC178853
0.5781 Remote Similarity NPC131770
0.5781 Remote Similarity NPC247546
0.5781 Remote Similarity NPC172086
0.5781 Remote Similarity NPC200618
0.5778 Remote Similarity NPC474699
0.5775 Remote Similarity NPC472019
0.5775 Remote Similarity NPC226602
0.5775 Remote Similarity NPC472020
0.5775 Remote Similarity NPC17935
0.5769 Remote Similarity NPC96322
0.5765 Remote Similarity NPC472744
0.5765 Remote Similarity NPC269684
0.5765 Remote Similarity NPC185256
0.5765 Remote Similarity NPC15091
0.5765 Remote Similarity NPC157328
0.5761 Remote Similarity NPC82633
0.5761 Remote Similarity NPC475900
0.5753 Remote Similarity NPC258690
0.5753 Remote Similarity NPC317651
0.575 Remote Similarity NPC217725
0.575 Remote Similarity NPC21220
0.575 Remote Similarity NPC125767
0.5747 Remote Similarity NPC474448
0.5745 Remote Similarity NPC471330
0.5745 Remote Similarity NPC472687
0.5745 Remote Similarity NPC99657
0.5745 Remote Similarity NPC203388
0.5745 Remote Similarity NPC471331
0.5733 Remote Similarity NPC241949
0.5732 Remote Similarity NPC475699
0.5732 Remote Similarity NPC469495
0.573 Remote Similarity NPC200580
0.573 Remote Similarity NPC67653
0.573 Remote Similarity NPC471459
0.5729 Remote Similarity NPC470172
0.5714 Remote Similarity NPC52700
0.5714 Remote Similarity NPC145045

  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 NPC10659 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
0.6176 Remote Similarity NPD8959 Approved
0.6027 Remote Similarity NPD9496 Clinical (unspecified phase)
0.597 Remote Similarity NPD3730 Approved
0.597 Remote Similarity NPD3728 Approved
0.5938 Remote Similarity NPD8964 Approved
0.589 Remote Similarity NPD371 Approved
0.5797 Remote Similarity NPD73 Approved
0.5789 Remote Similarity NPD1700 Approved
0.5789 Remote Similarity NPD229 Approved
0.5781 Remote Similarity NPD9005 Phase 3
0.5781 Remote Similarity NPD9004 Approved
0.5781 Remote Similarity NPD9003 Clinical (unspecified phase)
0.5758 Remote Similarity NPD9001 Clinical (unspecified phase)
0.5758 Remote Similarity NPD9002 Approved
0.5753 Remote Similarity NPD8961 Approved
0.5735 Remote Similarity NPD615 Clinical (unspecified phase)
0.5672 Remote Similarity NPD9010 Approved
0.5672 Remote Similarity NPD65 Approved
0.5672 Remote Similarity NPD9009 Approved
0.5672 Remote Similarity NPD66 Approved
0.5672 Remote Similarity NPD8960 Approved
0.5672 Remote Similarity NPD9008 Approved
0.5672 Remote Similarity NPD9011 Approved
0.5672 Remote Similarity NPD64 Approved
0.5672 Remote Similarity NPD9007 Approved
0.5672 Remote Similarity NPD72 Approved
0.5658 Remote Similarity NPD898 Approved
0.5658 Remote Similarity NPD896 Approved
0.5658 Remote Similarity NPD897 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