Structure

Physi-Chem Properties

Molecular Weight:  228.06
Volume:  203.315
LogP:  -0.261
LogD:  -0.333
LogS:  -2.509
# Rotatable Bonds:  1
TPSA:  82.06
# H-Bond Aceptor:  6
# H-Bond Donor:  1
# Rings:  3
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.579
Synthetic Accessibility Score:  5.286
Fsp3:  0.8
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.344
MDCK Permeability:  0.0001043307565851137
Pgp-inhibitor:  0.023
Pgp-substrate:  0.096
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.135
30% Bioavailability (F30%):  0.148

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.959
Plasma Protein Binding (PPB):  20.348556518554688%
Volume Distribution (VD):  0.582
Pgp-substrate:  80.85062408447266%

ADMET: Metabolism

CYP1A2-inhibitor:  0.022
CYP1A2-substrate:  0.368
CYP2C19-inhibitor:  0.019
CYP2C19-substrate:  0.207
CYP2C9-inhibitor:  0.002
CYP2C9-substrate:  0.027
CYP2D6-inhibitor:  0.005
CYP2D6-substrate:  0.115
CYP3A4-inhibitor:  0.614
CYP3A4-substrate:  0.256

ADMET: Excretion

Clearance (CL):  2.095
Half-life (T1/2):  0.85

ADMET: Toxicity

hERG Blockers:  0.008
Human Hepatotoxicity (H-HT):  0.87
Drug-inuced Liver Injury (DILI):  0.951
AMES Toxicity:  0.989
Rat Oral Acute Toxicity:  0.044
Maximum Recommended Daily Dose:  0.656
Skin Sensitization:  0.794
Carcinogencity:  0.864
Eye Corrosion:  0.473
Eye Irritation:  0.632
Respiratory Toxicity:  0.046

Download Data

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

  Natural Product: NPC125164

Natural Product ID:  NPC125164
Common Name*:   Lappaceolide B
IUPAC Name:   (3R,3aS,6aR)-6a-(hydroxymethyl)spiro[3a,6-dihydro-2H-furo[3,2-b]furan-3,4'-oxolane]-2',5-dione
Synonyms:  
Standard InCHIKey:  TVSNWZPMYISSOD-LPEHRKFASA-N
Standard InCHI:  InChI=1S/C10H12O6/c11-3-10-2-7(13)16-8(10)9(5-15-10)1-6(12)14-4-9/h8,11H,1-5H2/t8-,9-,10+/m0/s1
SMILES:  C1C(=O)OC[C@@]21CO[C@]1(CC(=O)O[C@@H]21)CO
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL445862
PubChem CID:   11572139
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001816] Furofurans

*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
NPO11357 Nephelium lappaceum Species Sapindaceae Eukaryota Seeds n.a. n.a. PMID[16180821]
NPO5258 Fagara zanthoxyloides n.a. n.a. n.a. n.a. n.a. n.a. PMID[22472691]
NPO21322 Plinia cauliflora Species Myrtaceae Eukaryota leaves n.a. n.a. PMID[32706260]
NPO11357 Nephelium lappaceum Species Sapindaceae Eukaryota n.a. n.a. Database[FooDB]
NPO358 Uncaria guianensis Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO4307 Canarium album Species Burseraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO358 Uncaria guianensis Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4307 Canarium album Species Burseraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO4307 Canarium album Species Burseraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO4307 Canarium album Species Burseraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO1933 Sideritis nutans Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO358 Uncaria guianensis Species Rubiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21322 Plinia cauliflora Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO816 Stenomesson miniatum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO6469 Clematis angustifolia Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3619 Ilex hainanensis Species Aquifoliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4676 Melicope sarcococca Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5868 Morus rubra Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5258 Fagara zanthoxyloides n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO12378 Streptomyces blastmyceticus Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO11357 Nephelium lappaceum Species Sapindaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3084 Xylopia brasiliensis Species Annonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4307 Canarium album Species Burseraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO10396 Pteris australis Species Pteridaceae 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
NPT19 Organism Escherichia coli Escherichia coli IZ = 11.0 mm PMID[470695]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa IZ = 12.0 mm PMID[470695]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus IZ = 11.0 mm PMID[470695]
NPT20 Organism Candida albicans Candida albicans IZ = 13.0 mm PMID[470695]
NPT330 Organism Trichophyton mentagrophytes Trichophyton mentagrophytes IZ = 13.0 mm PMID[470695]
NPT21 Organism Aspergillus niger Aspergillus niger IZ = 11.0 mm PMID[470695]
NPT19 Organism Escherichia coli Escherichia coli Activity_index = 0.1 n.a. PMID[470695]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa Activity_index = 0.2 n.a. PMID[470695]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus Activity_index = 0.1 n.a. PMID[470695]
NPT79 Organism Bacillus subtilis Bacillus subtilis Activity_index = 0.0 n.a. PMID[470695]
NPT20 Organism Candida albicans Candida albicans Activity_index = 0.3 n.a. PMID[470695]
NPT330 Organism Trichophyton mentagrophytes Trichophyton mentagrophytes Activity_index = 0.3 n.a. PMID[470695]
NPT21 Organism Aspergillus niger Aspergillus niger Activity_index = 0.1 n.a. PMID[470695]

☑ 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 NPC125164 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
0.8026 Intermediate Similarity NPC228411
0.7901 Intermediate Similarity NPC157328
0.7738 Intermediate Similarity NPC314364
0.7722 Intermediate Similarity NPC475616
0.7568 Intermediate Similarity NPC469925
0.7556 Intermediate Similarity NPC278028
0.7556 Intermediate Similarity NPC328180
0.75 Intermediate Similarity NPC478111
0.75 Intermediate Similarity NPC470014
0.7473 Intermediate Similarity NPC274695
0.7375 Intermediate Similarity NPC474003
0.7342 Intermediate Similarity NPC179922
0.7326 Intermediate Similarity NPC51662
0.7308 Intermediate Similarity NPC473699
0.7308 Intermediate Similarity NPC51249
0.7308 Intermediate Similarity NPC475232
0.7308 Intermediate Similarity NPC474100
0.7308 Intermediate Similarity NPC475260
0.7308 Intermediate Similarity NPC473775
0.7286 Intermediate Similarity NPC293692
0.7241 Intermediate Similarity NPC471221
0.7237 Intermediate Similarity NPC119838
0.7215 Intermediate Similarity NPC477867
0.7191 Intermediate Similarity NPC469627
0.7176 Intermediate Similarity NPC473791
0.7143 Intermediate Similarity NPC28526
0.7143 Intermediate Similarity NPC212340
0.7105 Intermediate Similarity NPC286842
0.7083 Intermediate Similarity NPC18433
0.7083 Intermediate Similarity NPC18044
0.7083 Intermediate Similarity NPC169089
0.7083 Intermediate Similarity NPC114365
0.7083 Intermediate Similarity NPC123070
0.7083 Intermediate Similarity NPC177518
0.7083 Intermediate Similarity NPC88890
0.7083 Intermediate Similarity NPC132304
0.7083 Intermediate Similarity NPC154962
0.7067 Intermediate Similarity NPC295256
0.7045 Intermediate Similarity NPC476435
0.701 Intermediate Similarity NPC469441
0.701 Intermediate Similarity NPC228311
0.701 Intermediate Similarity NPC168890
0.701 Intermediate Similarity NPC41674
0.7 Intermediate Similarity NPC215030
0.6951 Remote Similarity NPC214030
0.6951 Remote Similarity NPC83108
0.6939 Remote Similarity NPC290247
0.6939 Remote Similarity NPC469787
0.6939 Remote Similarity NPC469788
0.6939 Remote Similarity NPC176756
0.6933 Remote Similarity NPC314103
0.6932 Remote Similarity NPC186148
0.6915 Remote Similarity NPC253995
0.6915 Remote Similarity NPC211087
0.6907 Remote Similarity NPC473701
0.6907 Remote Similarity NPC473526
0.6892 Remote Similarity NPC10659
0.6892 Remote Similarity NPC469923
0.6889 Remote Similarity NPC65359
0.6883 Remote Similarity NPC57788
0.6883 Remote Similarity NPC53879
0.6875 Remote Similarity NPC292803
0.6869 Remote Similarity NPC220773
0.6869 Remote Similarity NPC278693
0.6869 Remote Similarity NPC329876
0.6869 Remote Similarity NPC167044
0.6854 Remote Similarity NPC177629
0.6854 Remote Similarity NPC58219
0.6842 Remote Similarity NPC476330
0.6818 Remote Similarity NPC476717
0.6813 Remote Similarity NPC474065
0.6813 Remote Similarity NPC474699
0.6806 Remote Similarity NPC220922
0.68 Remote Similarity NPC217041
0.6795 Remote Similarity NPC82315
0.6782 Remote Similarity NPC291310
0.6782 Remote Similarity NPC477434
0.6782 Remote Similarity NPC65133
0.6778 Remote Similarity NPC92974
0.6757 Remote Similarity NPC469921
0.675 Remote Similarity NPC470243
0.675 Remote Similarity NPC96322
0.6735 Remote Similarity NPC100078
0.6733 Remote Similarity NPC475463
0.6733 Remote Similarity NPC182185
0.6707 Remote Similarity NPC217725
0.6705 Remote Similarity NPC51267
0.6705 Remote Similarity NPC476715
0.6702 Remote Similarity NPC475785
0.6702 Remote Similarity NPC116683
0.6701 Remote Similarity NPC213528
0.6701 Remote Similarity NPC244969
0.6667 Remote Similarity NPC15091
0.6667 Remote Similarity NPC166079
0.6667 Remote Similarity NPC470009
0.6667 Remote Similarity NPC469922
0.663 Remote Similarity NPC208886
0.663 Remote Similarity NPC12172
0.6629 Remote Similarity NPC475729
0.6629 Remote Similarity NPC475491
0.6629 Remote Similarity NPC474215
0.6629 Remote Similarity NPC469626
0.6623 Remote Similarity NPC469926
0.6618 Remote Similarity NPC46254
0.6602 Remote Similarity NPC98870
0.6596 Remote Similarity NPC470191
0.6593 Remote Similarity NPC200580
0.6593 Remote Similarity NPC477443
0.6593 Remote Similarity NPC477440
0.6591 Remote Similarity NPC151176
0.6591 Remote Similarity NPC3464
0.6591 Remote Similarity NPC475963
0.6591 Remote Similarity NPC115995
0.6579 Remote Similarity NPC235788
0.6575 Remote Similarity NPC61567
0.6571 Remote Similarity NPC277878
0.6562 Remote Similarity NPC472144
0.6559 Remote Similarity NPC81419
0.6559 Remote Similarity NPC475788
0.6559 Remote Similarity NPC179746
0.6556 Remote Similarity NPC190753
0.6552 Remote Similarity NPC311642
0.6552 Remote Similarity NPC100366
0.6552 Remote Similarity NPC242771
0.6552 Remote Similarity NPC164289
0.6531 Remote Similarity NPC225353
0.6526 Remote Similarity NPC470883
0.6526 Remote Similarity NPC158416
0.6526 Remote Similarity NPC39859
0.6526 Remote Similarity NPC475765
0.6526 Remote Similarity NPC76862
0.6526 Remote Similarity NPC476009
0.6522 Remote Similarity NPC477444
0.6522 Remote Similarity NPC206614
0.6522 Remote Similarity NPC470114
0.6522 Remote Similarity NPC246173
0.6522 Remote Similarity NPC474323
0.6522 Remote Similarity NPC477442
0.6522 Remote Similarity NPC477433
0.6517 Remote Similarity NPC473350
0.6512 Remote Similarity NPC134227
0.65 Remote Similarity NPC306776
0.65 Remote Similarity NPC475062
0.6489 Remote Similarity NPC309127
0.6489 Remote Similarity NPC470424
0.6489 Remote Similarity NPC247877
0.6486 Remote Similarity NPC179624
0.6484 Remote Similarity NPC221993
0.6479 Remote Similarity NPC196612
0.6465 Remote Similarity NPC110989
0.6458 Remote Similarity NPC134454
0.6458 Remote Similarity NPC311904
0.6458 Remote Similarity NPC472145
0.6458 Remote Similarity NPC17326
0.6456 Remote Similarity NPC32148
0.6452 Remote Similarity NPC184463
0.6452 Remote Similarity NPC475878
0.6452 Remote Similarity NPC475881
0.6452 Remote Similarity NPC70251
0.6444 Remote Similarity NPC470657
0.6444 Remote Similarity NPC475019
0.6444 Remote Similarity NPC474949
0.6438 Remote Similarity NPC198377
0.6437 Remote Similarity NPC475743
0.6429 Remote Similarity NPC259654
0.6429 Remote Similarity NPC162024
0.6429 Remote Similarity NPC298266
0.6421 Remote Similarity NPC475900
0.6413 Remote Similarity NPC471459
0.6413 Remote Similarity NPC473564
0.6413 Remote Similarity NPC478110
0.6413 Remote Similarity NPC67653
0.6404 Remote Similarity NPC474780
0.64 Remote Similarity NPC203659
0.64 Remote Similarity NPC470363
0.6392 Remote Similarity NPC471144
0.6383 Remote Similarity NPC475912
0.6383 Remote Similarity NPC472237
0.6383 Remote Similarity NPC153590
0.6383 Remote Similarity NPC212486
0.6383 Remote Similarity NPC472238
0.6374 Remote Similarity NPC239938
0.6374 Remote Similarity NPC31349
0.6364 Remote Similarity NPC268243
0.6364 Remote Similarity NPC325773
0.6364 Remote Similarity NPC148740
0.6364 Remote Similarity NPC258690
0.6364 Remote Similarity NPC102156
0.6364 Remote Similarity NPC317651
0.6364 Remote Similarity NPC471254
0.6354 Remote Similarity NPC21302
0.6354 Remote Similarity NPC235109
0.6354 Remote Similarity NPC11396
0.6354 Remote Similarity NPC126156
0.6354 Remote Similarity NPC193785
0.6354 Remote Similarity NPC142529
0.6354 Remote Similarity NPC91771
0.6353 Remote Similarity NPC307865
0.6344 Remote Similarity NPC185529
0.6344 Remote Similarity NPC472146

  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 NPC125164 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
0.7237 Intermediate Similarity NPD229 Approved
0.7083 Intermediate Similarity NPD4057 Clinical (unspecified phase)
0.7083 Intermediate Similarity NPD4056 Clinical (unspecified phase)
0.7067 Intermediate Similarity NPD9496 Clinical (unspecified phase)
0.6901 Remote Similarity NPD73 Approved
0.6806 Remote Similarity NPD8959 Approved
0.6771 Remote Similarity NPD1700 Approved
0.6571 Remote Similarity NPD9008 Approved
0.6571 Remote Similarity NPD9007 Approved
0.6571 Remote Similarity NPD72 Approved
0.6571 Remote Similarity NPD66 Approved
0.6571 Remote Similarity NPD9011 Approved
0.6571 Remote Similarity NPD65 Approved
0.6571 Remote Similarity NPD64 Approved
0.6571 Remote Similarity NPD8960 Approved
0.6571 Remote Similarity NPD9010 Approved
0.6571 Remote Similarity NPD9009 Approved
0.6456 Remote Similarity NPD896 Approved
0.6456 Remote Similarity NPD898 Approved
0.6456 Remote Similarity NPD897 Approved
0.6364 Remote Similarity NPD8961 Approved
0.6164 Remote Similarity NPD3728 Approved
0.6164 Remote Similarity NPD3730 Approved
0.6076 Remote Similarity NPD7909 Approved
0.5972 Remote Similarity NPD9002 Approved
0.5972 Remote Similarity NPD9001 Clinical (unspecified phase)
0.5946 Remote Similarity NPD3729 Clinical (unspecified phase)
0.5938 Remote Similarity NPD7983 Approved
0.593 Remote Similarity NPD376 Approved
0.593 Remote Similarity NPD11 Approved
0.5918 Remote Similarity NPD1698 Clinical (unspecified phase)
0.5905 Remote Similarity NPD5345 Clinical (unspecified phase)
0.5882 Remote Similarity NPD8083 Approved
0.5882 Remote Similarity NPD8139 Approved
0.5882 Remote Similarity NPD8086 Approved
0.5882 Remote Similarity NPD8084 Approved
0.5882 Remote Similarity NPD8138 Approved
0.5882 Remote Similarity NPD8082 Approved
0.5882 Remote Similarity NPD8085 Approved
0.5825 Remote Similarity NPD8276 Approved
0.5825 Remote Similarity NPD8275 Approved
0.5789 Remote Similarity NPD2267 Suspended
0.5775 Remote Similarity NPD9005 Phase 3
0.5775 Remote Similarity NPD9003 Clinical (unspecified phase)
0.5775 Remote Similarity NPD9004 Approved
0.5775 Remote Similarity NPD2266 Phase 2
0.5769 Remote Similarity NPD8081 Approved
0.5753 Remote Similarity NPD9638 Phase 2
0.5735 Remote Similarity NPD8957 Approved
0.573 Remote Similarity NPD4238 Approved
0.573 Remote Similarity NPD4802 Phase 2
0.5714 Remote Similarity NPD8393 Approved
0.5698 Remote Similarity NPD3181 Approved
0.5694 Remote Similarity NPD9126 Approved
0.5694 Remote Similarity NPD71 Approved
0.5694 Remote Similarity NPD9129 Approved
0.5694 Remote Similarity NPD8964 Approved
0.5667 Remote Similarity NPD7329 Approved
0.566 Remote Similarity NPD7899 Clinical (unspecified phase)
0.5657 Remote Similarity NPD5282 Discontinued
0.5652 Remote Similarity NPD7345 Approved
0.5648 Remote Similarity NPD6371 Approved
0.5619 Remote Similarity NPD8170 Clinical (unspecified phase)

  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