Structure

Physi-Chem Properties

Molecular Weight:  307.9
Volume:  203.902
LogP:  3.821
LogD:  3.293
LogS:  -4.586
# Rotatable Bonds:  3
TPSA:  26.3
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.744
Synthetic Accessibility Score:  3.26
Fsp3:  0.444
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.436
MDCK Permeability:  2.386659434705507e-05
Pgp-inhibitor:  0.008
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.134
30% Bioavailability (F30%):  0.965

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.27
Plasma Protein Binding (PPB):  96.8982925415039%
Volume Distribution (VD):  0.687
Pgp-substrate:  7.324736595153809%

ADMET: Metabolism

CYP1A2-inhibitor:  0.982
CYP1A2-substrate:  0.664
CYP2C19-inhibitor:  0.891
CYP2C19-substrate:  0.18
CYP2C9-inhibitor:  0.867
CYP2C9-substrate:  0.685
CYP2D6-inhibitor:  0.933
CYP2D6-substrate:  0.165
CYP3A4-inhibitor:  0.616
CYP3A4-substrate:  0.159

ADMET: Excretion

Clearance (CL):  1.232
Half-life (T1/2):  0.419

ADMET: Toxicity

hERG Blockers:  0.008
Human Hepatotoxicity (H-HT):  0.766
Drug-inuced Liver Injury (DILI):  0.827
AMES Toxicity:  0.895
Rat Oral Acute Toxicity:  0.728
Maximum Recommended Daily Dose:  0.247
Skin Sensitization:  0.948
Carcinogencity:  0.873
Eye Corrosion:  0.902
Eye Irritation:  0.954
Respiratory Toxicity:  0.965

Download Data

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

  Natural Product: NPC173409

Natural Product ID:  NPC173409
Common Name*:   Fimbrolide
IUPAC Name:   (5E)-4-bromo-5-(bromomethylidene)-3-butylfuran-2-one
Synonyms:   Fimbrolide
Standard InCHIKey:  UVJAGAXWVHGYRW-FNORWQNLSA-N
Standard InCHI:  InChI=1S/C9H10Br2O2/c1-2-3-4-6-8(11)7(5-10)13-9(6)12/h5H,2-4H2,1H3/b7-5+
SMILES:  CCCCC1=C(/C(=CBr)/OC1=O)Br
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL503333
PubChem CID:   9796693
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
NPO32988 antarctic peninsula Species n.a. n.a. n.a. n.a. n.a. PMID[15332845]

☑ 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 IZ = 7.0 mm PMID[506461]

☑ 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 NPC173409 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
1.0 High Similarity NPC53136
0.9661 High Similarity NPC217537
0.8939 High Similarity NPC112983
0.8939 High Similarity NPC162571
0.8636 High Similarity NPC494
0.8594 High Similarity NPC475110
0.8429 Intermediate Similarity NPC238554
0.8429 Intermediate Similarity NPC225022
0.8261 Intermediate Similarity NPC146583
0.8143 Intermediate Similarity NPC177030
0.7857 Intermediate Similarity NPC269103
0.7857 Intermediate Similarity NPC124072
0.7808 Intermediate Similarity NPC228902
0.7808 Intermediate Similarity NPC24827
0.76 Intermediate Similarity NPC286816
0.76 Intermediate Similarity NPC199134
0.7465 Intermediate Similarity NPC475113
0.7465 Intermediate Similarity NPC299932
0.7273 Intermediate Similarity NPC133600
0.7206 Intermediate Similarity NPC132243
0.7162 Intermediate Similarity NPC188354
0.7067 Intermediate Similarity NPC469414
0.7067 Intermediate Similarity NPC329826
0.7 Intermediate Similarity NPC133904
0.7 Intermediate Similarity NPC131174
0.6944 Remote Similarity NPC287705
0.6944 Remote Similarity NPC218477
0.6923 Remote Similarity NPC478117
0.6901 Remote Similarity NPC248125
0.6883 Remote Similarity NPC68156
0.6818 Remote Similarity NPC86948
0.6812 Remote Similarity NPC151648
0.6795 Remote Similarity NPC85743
0.6795 Remote Similarity NPC102065
0.6761 Remote Similarity NPC220766
0.6761 Remote Similarity NPC182794
0.6712 Remote Similarity NPC474823
0.6667 Remote Similarity NPC429928
0.6667 Remote Similarity NPC191233
0.6667 Remote Similarity NPC173157
0.6667 Remote Similarity NPC186531
0.6667 Remote Similarity NPC84038
0.6667 Remote Similarity NPC315115
0.6667 Remote Similarity NPC133098
0.6622 Remote Similarity NPC475004
0.6622 Remote Similarity NPC232812
0.6579 Remote Similarity NPC474705
0.6575 Remote Similarity NPC21998
0.6575 Remote Similarity NPC203335
0.6533 Remote Similarity NPC67183
0.6533 Remote Similarity NPC37929
0.6533 Remote Similarity NPC64234
0.6528 Remote Similarity NPC470688
0.6528 Remote Similarity NPC471556
0.6522 Remote Similarity NPC286189
0.65 Remote Similarity NPC103560
0.6486 Remote Similarity NPC313444
0.6479 Remote Similarity NPC210303
0.6479 Remote Similarity NPC155849
0.6479 Remote Similarity NPC68110
0.6479 Remote Similarity NPC179087
0.6479 Remote Similarity NPC44343
0.6479 Remote Similarity NPC473737
0.6462 Remote Similarity NPC191643
0.6456 Remote Similarity NPC316324
0.641 Remote Similarity NPC478191
0.641 Remote Similarity NPC478194
0.641 Remote Similarity NPC478196
0.641 Remote Similarity NPC478192
0.641 Remote Similarity NPC478193
0.641 Remote Similarity NPC478195
0.64 Remote Similarity NPC265574
0.64 Remote Similarity NPC470693
0.64 Remote Similarity NPC473277
0.6377 Remote Similarity NPC189700
0.6364 Remote Similarity NPC287878
0.6364 Remote Similarity NPC144419
0.6351 Remote Similarity NPC132286
0.6341 Remote Similarity NPC42470
0.6338 Remote Similarity NPC15193
0.6329 Remote Similarity NPC123360
0.6316 Remote Similarity NPC316029
0.6316 Remote Similarity NPC315285
0.6316 Remote Similarity NPC315597
0.6301 Remote Similarity NPC471565
0.6301 Remote Similarity NPC476589
0.6301 Remote Similarity NPC471566
0.6282 Remote Similarity NPC476355
0.6282 Remote Similarity NPC117746
0.6282 Remote Similarity NPC474758
0.6282 Remote Similarity NPC259599
0.6282 Remote Similarity NPC15499
0.6282 Remote Similarity NPC294434
0.6269 Remote Similarity NPC478120
0.6269 Remote Similarity NPC218486
0.6267 Remote Similarity NPC470256
0.6267 Remote Similarity NPC470032
0.6267 Remote Similarity NPC238223
0.6267 Remote Similarity NPC280374
0.6267 Remote Similarity NPC79220
0.6267 Remote Similarity NPC276290
0.625 Remote Similarity NPC180290
0.625 Remote Similarity NPC474658
0.625 Remote Similarity NPC10572
0.625 Remote Similarity NPC135698
0.625 Remote Similarity NPC473825
0.625 Remote Similarity NPC54996
0.625 Remote Similarity NPC234084
0.625 Remote Similarity NPC57744
0.6234 Remote Similarity NPC163003
0.6216 Remote Similarity NPC116013
0.6216 Remote Similarity NPC37382
0.6203 Remote Similarity NPC329852
0.6197 Remote Similarity NPC309408
0.6197 Remote Similarity NPC130953
0.6197 Remote Similarity NPC79756
0.6176 Remote Similarity NPC49028
0.6173 Remote Similarity NPC315765
0.6173 Remote Similarity NPC299235
0.6173 Remote Similarity NPC471220
0.6173 Remote Similarity NPC128276
0.6164 Remote Similarity NPC471460
0.6164 Remote Similarity NPC475618
0.6163 Remote Similarity NPC469861
0.6163 Remote Similarity NPC469860
0.6163 Remote Similarity NPC130436
0.6154 Remote Similarity NPC269206
0.6154 Remote Similarity NPC295633
0.6154 Remote Similarity NPC236338
0.6154 Remote Similarity NPC58956
0.6133 Remote Similarity NPC225272
0.6133 Remote Similarity NPC472266
0.6133 Remote Similarity NPC194871
0.6125 Remote Similarity NPC27205
0.6119 Remote Similarity NPC473784
0.6098 Remote Similarity NPC63326
0.6098 Remote Similarity NPC472965
0.6098 Remote Similarity NPC264227
0.6098 Remote Similarity NPC178277
0.6098 Remote Similarity NPC265980
0.6098 Remote Similarity NPC63649
0.6098 Remote Similarity NPC150646
0.6087 Remote Similarity NPC150717
0.6087 Remote Similarity NPC221763
0.6076 Remote Similarity NPC140287
0.6076 Remote Similarity NPC470686
0.6071 Remote Similarity NPC8161
0.6049 Remote Similarity NPC53581
0.6049 Remote Similarity NPC103987
0.6049 Remote Similarity NPC187568
0.6049 Remote Similarity NPC41780
0.6047 Remote Similarity NPC281172
0.6032 Remote Similarity NPC270706
0.6027 Remote Similarity NPC2328
0.6027 Remote Similarity NPC217940
0.6027 Remote Similarity NPC474774
0.6026 Remote Similarity NPC129665
0.6026 Remote Similarity NPC257618
0.6024 Remote Similarity NPC474510
0.6023 Remote Similarity NPC475739
0.6023 Remote Similarity NPC472302
0.6 Remote Similarity NPC308294
0.6 Remote Similarity NPC142423
0.5976 Remote Similarity NPC108816
0.5976 Remote Similarity NPC93763
0.5976 Remote Similarity NPC222210
0.5976 Remote Similarity NPC63445
0.5974 Remote Similarity NPC236208
0.5974 Remote Similarity NPC88877
0.5974 Remote Similarity NPC476591
0.5972 Remote Similarity NPC98519
0.597 Remote Similarity NPC216407
0.597 Remote Similarity NPC151919
0.5955 Remote Similarity NPC95364
0.5955 Remote Similarity NPC142159
0.5952 Remote Similarity NPC325031
0.5952 Remote Similarity NPC471325
0.5938 Remote Similarity NPC128280
0.5926 Remote Similarity NPC235906
0.5926 Remote Similarity NPC473223
0.5909 Remote Similarity NPC27264
0.5904 Remote Similarity NPC270126
0.5904 Remote Similarity NPC471299
0.589 Remote Similarity NPC68044
0.5882 Remote Similarity NPC94875
0.5882 Remote Similarity NPC473529
0.5882 Remote Similarity NPC475159
0.5882 Remote Similarity NPC471326
0.5882 Remote Similarity NPC35556
0.5882 Remote Similarity NPC131002
0.5882 Remote Similarity NPC11332
0.5882 Remote Similarity NPC173609
0.5882 Remote Similarity NPC473712
0.5882 Remote Similarity NPC145914
0.5882 Remote Similarity NPC329829
0.5882 Remote Similarity NPC73310
0.5882 Remote Similarity NPC473780
0.5882 Remote Similarity NPC221231
0.5882 Remote Similarity NPC180363
0.5882 Remote Similarity NPC65930

  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 NPC173409 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
0.6061 Remote Similarity NPD6927 Phase 3
0.5882 Remote Similarity NPD5209 Approved
0.5867 Remote Similarity NPD2685 Clinical (unspecified phase)
0.5854 Remote Similarity NPD4756 Discovery
0.5802 Remote Similarity NPD8039 Approved
0.5781 Remote Similarity NPD3174 Discontinued
0.5698 Remote Similarity NPD4752 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