Structure

Physi-Chem Properties

Molecular Weight:  214.08
Volume:  209.002
LogP:  0.831
LogD:  0.976
LogS:  -0.664
# Rotatable Bonds:  5
TPSA:  79.9
# H-Bond Aceptor:  5
# H-Bond Donor:  2
# Rings:  1
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.74
Synthetic Accessibility Score:  3.814
Fsp3:  0.5
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:  -4.807
MDCK Permeability:  7.384464697679505e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.414
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.008
30% Bioavailability (F30%):  0.959

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.165
Plasma Protein Binding (PPB):  57.737953186035156%
Volume Distribution (VD):  0.851
Pgp-substrate:  53.78996276855469%

ADMET: Metabolism

CYP1A2-inhibitor:  0.09
CYP1A2-substrate:  0.089
CYP2C19-inhibitor:  0.033
CYP2C19-substrate:  0.074
CYP2C9-inhibitor:  0.03
CYP2C9-substrate:  0.825
CYP2D6-inhibitor:  0.049
CYP2D6-substrate:  0.414
CYP3A4-inhibitor:  0.026
CYP3A4-substrate:  0.224

ADMET: Excretion

Clearance (CL):  7.805
Half-life (T1/2):  0.903

ADMET: Toxicity

hERG Blockers:  0.011
Human Hepatotoxicity (H-HT):  0.237
Drug-inuced Liver Injury (DILI):  0.587
AMES Toxicity:  0.053
Rat Oral Acute Toxicity:  0.13
Maximum Recommended Daily Dose:  0.822
Skin Sensitization:  0.134
Carcinogencity:  0.918
Eye Corrosion:  0.736
Eye Irritation:  0.898
Respiratory Toxicity:  0.091

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

  Natural Product: NPC276299

Natural Product ID:  NPC276299
Common Name*:   Botryolide-E
IUPAC Name:   [(2R,4S)-4-hydroxy-4-[(2S)-5-oxo-2H-furan-2-yl]butan-2-yl] acetate
Synonyms:   Botryolide-E
Standard InCHIKey:  ITCOWOVATIICJS-YEPSODPASA-N
Standard InCHI:  InChI=1S/C10H14O5/c1-6(14-7(2)11)5-8(12)9-3-4-10(13)15-9/h3-4,6,8-9,12H,5H2,1-2H3/t6-,8+,9+/m1/s1
SMILES:  C[C@H](C[C@@H]([C@@H]1C=CC(=O)O1)O)OC(=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1668900
PubChem CID:   53324482
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001983] Dihydrofurans
        • [CHEMONTID:0001982] Furanones
          • [CHEMONTID:0002223] Butenolides

*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
NPO26085 Salacia kraussii Species Celastraceae Eukaryota n.a. n.a. n.a. PMID[9644053]
NPO8522 Dicentra cucullaria Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO8522 Dicentra cucullaria Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8522 Dicentra cucullaria Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO26512 Lactarius pallidus Species Russulaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8522 Dicentra cucullaria Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26112 Arenosclera brasiliensis Species Callyspongiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26085 Salacia kraussii Species Celastraceae 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
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 25.0 ug.mL-1 PMID[483294]
NPT79 Organism Bacillus subtilis Bacillus subtilis MIC = 6.25 ug.mL-1 PMID[483294]
NPT17 Organism Staphylococcus epidermidis Staphylococcus epidermidis MIC = 50.0 ug.mL-1 PMID[483294]
NPT19 Organism Escherichia coli Escherichia coli MIC = 12.5 ug.mL-1 PMID[483294]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa MIC = 50.0 ug.mL-1 PMID[483294]
NPT173 Organism Klebsiella pneumoniae Klebsiella pneumoniae MIC = 50.0 ug.mL-1 PMID[483294]
NPT923 Organism Rhizopus oryzae Rhizopus oryzae IZ = 14.0 mm PMID[483294]
NPT21 Organism Aspergillus niger Aspergillus niger IZ = 10.0 mm PMID[483294]
NPT20 Organism Candida albicans Candida albicans IZ = 12.0 mm PMID[483294]
NPT312 Organism Saccharomyces cerevisiae Saccharomyces cerevisiae IZ = 8.0 mm PMID[483294]

☑ 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 NPC276299 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
0.9206 High Similarity NPC19769
0.8906 High Similarity NPC470123
0.8788 High Similarity NPC63873
0.8769 High Similarity NPC201356
0.8615 High Similarity NPC96414
0.8438 Intermediate Similarity NPC26810
0.8382 Intermediate Similarity NPC475982
0.8209 Intermediate Similarity NPC146811
0.8182 Intermediate Similarity NPC148233
0.8182 Intermediate Similarity NPC470808
0.8182 Intermediate Similarity NPC25747
0.8169 Intermediate Similarity NPC107654
0.8125 Intermediate Similarity NPC97570
0.8125 Intermediate Similarity NPC302564
0.8088 Intermediate Similarity NPC122627
0.8082 Intermediate Similarity NPC474026
0.806 Intermediate Similarity NPC282760
0.8 Intermediate Similarity NPC202011
0.8 Intermediate Similarity NPC26223
0.7973 Intermediate Similarity NPC248775
0.7973 Intermediate Similarity NPC318481
0.7969 Intermediate Similarity NPC187770
0.7941 Intermediate Similarity NPC37382
0.7941 Intermediate Similarity NPC124586
0.7937 Intermediate Similarity NPC230296
0.7917 Intermediate Similarity NPC315843
0.791 Intermediate Similarity NPC308457
0.7867 Intermediate Similarity NPC1180
0.7867 Intermediate Similarity NPC470149
0.7867 Intermediate Similarity NPC180725
0.7867 Intermediate Similarity NPC470148
0.7838 Intermediate Similarity NPC475711
0.7826 Intermediate Similarity NPC478100
0.7812 Intermediate Similarity NPC319423
0.7808 Intermediate Similarity NPC478192
0.7808 Intermediate Similarity NPC478193
0.7808 Intermediate Similarity NPC478191
0.7808 Intermediate Similarity NPC161038
0.7808 Intermediate Similarity NPC478196
0.7808 Intermediate Similarity NPC478195
0.7808 Intermediate Similarity NPC478194
0.7794 Intermediate Similarity NPC273600
0.7778 Intermediate Similarity NPC284006
0.7763 Intermediate Similarity NPC470147
0.7763 Intermediate Similarity NPC133226
0.7761 Intermediate Similarity NPC473737
0.7746 Intermediate Similarity NPC476037
0.7746 Intermediate Similarity NPC476012
0.7714 Intermediate Similarity NPC474823
0.7714 Intermediate Similarity NPC475760
0.7681 Intermediate Similarity NPC478101
0.7671 Intermediate Similarity NPC474280
0.7671 Intermediate Similarity NPC326504
0.7671 Intermediate Similarity NPC473489
0.7662 Intermediate Similarity NPC297440
0.7639 Intermediate Similarity NPC293114
0.7639 Intermediate Similarity NPC316185
0.7632 Intermediate Similarity NPC99651
0.7606 Intermediate Similarity NPC475004
0.76 Intermediate Similarity NPC275530
0.7571 Intermediate Similarity NPC25298
0.7571 Intermediate Similarity NPC478097
0.7568 Intermediate Similarity NPC473582
0.7568 Intermediate Similarity NPC473948
0.7564 Intermediate Similarity NPC474959
0.7564 Intermediate Similarity NPC11383
0.7564 Intermediate Similarity NPC475046
0.7564 Intermediate Similarity NPC251026
0.7564 Intermediate Similarity NPC310450
0.7536 Intermediate Similarity NPC478098
0.7536 Intermediate Similarity NPC478099
0.7534 Intermediate Similarity NPC327383
0.7534 Intermediate Similarity NPC185186
0.7534 Intermediate Similarity NPC329890
0.7534 Intermediate Similarity NPC329914
0.75 Intermediate Similarity NPC475073
0.75 Intermediate Similarity NPC473471
0.7468 Intermediate Similarity NPC142111
0.7468 Intermediate Similarity NPC229799
0.7468 Intermediate Similarity NPC473315
0.7468 Intermediate Similarity NPC286770
0.7468 Intermediate Similarity NPC315559
0.7468 Intermediate Similarity NPC284472
0.7467 Intermediate Similarity NPC301207
0.7467 Intermediate Similarity NPC127118
0.7467 Intermediate Similarity NPC326661
0.7467 Intermediate Similarity NPC209113
0.7463 Intermediate Similarity NPC81896
0.7463 Intermediate Similarity NPC321919
0.7436 Intermediate Similarity NPC469469
0.7432 Intermediate Similarity NPC114727
0.7432 Intermediate Similarity NPC476590
0.7429 Intermediate Similarity NPC248125
0.7429 Intermediate Similarity NPC475675
0.7429 Intermediate Similarity NPC475555
0.7424 Intermediate Similarity NPC474084
0.7407 Intermediate Similarity NPC69082
0.7407 Intermediate Similarity NPC279267
0.7397 Intermediate Similarity NPC475762
0.7391 Intermediate Similarity NPC475221
0.7385 Intermediate Similarity NPC472808
0.7385 Intermediate Similarity NPC324224
0.7375 Intermediate Similarity NPC163093
0.7375 Intermediate Similarity NPC473308
0.7368 Intermediate Similarity NPC49302
0.7368 Intermediate Similarity NPC233071
0.7368 Intermediate Similarity NPC474278
0.7368 Intermediate Similarity NPC51809
0.7368 Intermediate Similarity NPC474818
0.7368 Intermediate Similarity NPC176329
0.7368 Intermediate Similarity NPC125365
0.7361 Intermediate Similarity NPC130618
0.7342 Intermediate Similarity NPC313677
0.7333 Intermediate Similarity NPC327041
0.7333 Intermediate Similarity NPC285840
0.7317 Intermediate Similarity NPC178215
0.7313 Intermediate Similarity NPC159650
0.7313 Intermediate Similarity NPC22897
0.7284 Intermediate Similarity NPC103284
0.7284 Intermediate Similarity NPC1083
0.7284 Intermediate Similarity NPC473478
0.7284 Intermediate Similarity NPC182383
0.7284 Intermediate Similarity NPC477014
0.7284 Intermediate Similarity NPC283085
0.7284 Intermediate Similarity NPC231009
0.7284 Intermediate Similarity NPC107986
0.7284 Intermediate Similarity NPC120398
0.7284 Intermediate Similarity NPC82795
0.7284 Intermediate Similarity NPC477013
0.7284 Intermediate Similarity NPC286338
0.7284 Intermediate Similarity NPC132496
0.7284 Intermediate Similarity NPC110710
0.7284 Intermediate Similarity NPC66346
0.7284 Intermediate Similarity NPC473669
0.7284 Intermediate Similarity NPC473651
0.7284 Intermediate Similarity NPC223871
0.7284 Intermediate Similarity NPC471567
0.7284 Intermediate Similarity NPC322529
0.7273 Intermediate Similarity NPC28049
0.7273 Intermediate Similarity NPC477314
0.7273 Intermediate Similarity NPC279214
0.7273 Intermediate Similarity NPC279532
0.7273 Intermediate Similarity NPC221095
0.725 Intermediate Similarity NPC44261
0.725 Intermediate Similarity NPC253801
0.7246 Intermediate Similarity NPC68110
0.7237 Intermediate Similarity NPC68819
0.7237 Intermediate Similarity NPC190400
0.7237 Intermediate Similarity NPC203277
0.7237 Intermediate Similarity NPC49392
0.7237 Intermediate Similarity NPC188860
0.7229 Intermediate Similarity NPC233551
0.7229 Intermediate Similarity NPC21208
0.7229 Intermediate Similarity NPC280621
0.7229 Intermediate Similarity NPC48338
0.7229 Intermediate Similarity NPC20339
0.7229 Intermediate Similarity NPC40376
0.7222 Intermediate Similarity NPC238223
0.7222 Intermediate Similarity NPC310210
0.7215 Intermediate Similarity NPC150502
0.72 Intermediate Similarity NPC474545
0.7195 Intermediate Similarity NPC171174
0.7195 Intermediate Similarity NPC134885
0.7195 Intermediate Similarity NPC208473
0.7195 Intermediate Similarity NPC240695
0.7195 Intermediate Similarity NPC475581
0.7195 Intermediate Similarity NPC112685
0.7195 Intermediate Similarity NPC142117
0.7195 Intermediate Similarity NPC103523
0.7195 Intermediate Similarity NPC210218
0.7195 Intermediate Similarity NPC204686
0.7195 Intermediate Similarity NPC62118
0.7195 Intermediate Similarity NPC308412
0.7195 Intermediate Similarity NPC232555
0.7195 Intermediate Similarity NPC231096
0.7195 Intermediate Similarity NPC477015
0.7195 Intermediate Similarity NPC134865
0.7195 Intermediate Similarity NPC134807
0.7195 Intermediate Similarity NPC219498
0.7195 Intermediate Similarity NPC473687
0.7195 Intermediate Similarity NPC114694
0.7195 Intermediate Similarity NPC107717
0.7195 Intermediate Similarity NPC47937
0.7179 Intermediate Similarity NPC475210
0.7164 Intermediate Similarity NPC223679
0.716 Intermediate Similarity NPC475035
0.716 Intermediate Similarity NPC266718
0.716 Intermediate Similarity NPC156804
0.7143 Intermediate Similarity NPC114464
0.7143 Intermediate Similarity NPC133450
0.7125 Intermediate Similarity NPC65930
0.7125 Intermediate Similarity NPC94875
0.7125 Intermediate Similarity NPC180363
0.7125 Intermediate Similarity NPC145914
0.7125 Intermediate Similarity NPC473529
0.7125 Intermediate Similarity NPC473780
0.7125 Intermediate Similarity NPC11332
0.7125 Intermediate Similarity NPC329829
0.7125 Intermediate Similarity NPC73310
0.7125 Intermediate Similarity NPC475159

  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 NPC276299 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
0.7969 Intermediate Similarity NPD9119 Approved
0.7969 Intermediate Similarity NPD69 Approved
0.7812 Intermediate Similarity NPD9118 Approved
0.7164 Intermediate Similarity NPD585 Clinical (unspecified phase)
0.686 Remote Similarity NPD7838 Discovery
0.6667 Remote Similarity NPD6109 Phase 1
0.6548 Remote Similarity NPD6400 Clinical (unspecified phase)
0.6477 Remote Similarity NPD46 Approved
0.6477 Remote Similarity NPD6698 Approved
0.6265 Remote Similarity NPD5790 Clinical (unspecified phase)
0.625 Remote Similarity NPD4246 Clinical (unspecified phase)
0.6211 Remote Similarity NPD5344 Discontinued
0.6184 Remote Similarity NPD4247 Clinical (unspecified phase)
0.617 Remote Similarity NPD4225 Approved
0.6133 Remote Similarity NPD2685 Clinical (unspecified phase)
0.6024 Remote Similarity NPD4271 Approved
0.6024 Remote Similarity NPD4268 Approved
0.6022 Remote Similarity NPD1698 Clinical (unspecified phase)
0.6 Remote Similarity NPD8029 Clinical (unspecified phase)
0.6 Remote Similarity NPD3197 Phase 1
0.5934 Remote Similarity NPD5785 Approved
0.5882 Remote Similarity NPD4819 Approved
0.5882 Remote Similarity NPD4821 Approved
0.5882 Remote Similarity NPD4820 Approved
0.5882 Remote Similarity NPD6927 Phase 3
0.5882 Remote Similarity NPD4822 Approved
0.587 Remote Similarity NPD7983 Approved
0.5862 Remote Similarity NPD7154 Phase 3
0.5843 Remote Similarity NPD4249 Approved
0.5842 Remote Similarity NPD6686 Approved
0.5789 Remote Similarity NPD4792 Clinical (unspecified phase)
0.5778 Remote Similarity NPD4250 Approved
0.5778 Remote Similarity NPD4251 Approved
0.5773 Remote Similarity NPD6648 Approved
0.5747 Remote Similarity NPD5209 Approved
0.5743 Remote Similarity NPD7899 Clinical (unspecified phase)
0.573 Remote Similarity NPD5363 Approved
0.573 Remote Similarity NPD6082 Clinical (unspecified phase)
0.5728 Remote Similarity NPD6371 Approved
0.5672 Remote Similarity NPD5343 Approved
0.5606 Remote Similarity NPD4222 Approved
0.5606 Remote Similarity NPD39 Approved
0.56 Remote Similarity NPD9120 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