Structure

Physi-Chem Properties

Molecular Weight:  413.9
Volume:  259.431
LogP:  3.55
LogD:  1.905
LogS:  -3.575
# Rotatable Bonds:  5
TPSA:  52.6
# H-Bond Aceptor:  4
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.523
Synthetic Accessibility Score:  3.912
Fsp3:  0.455
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.393
MDCK Permeability:  2.2730917407898232e-05
Pgp-inhibitor:  0.948
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.978
30% Bioavailability (F30%):  0.99

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.478
Plasma Protein Binding (PPB):  96.26824188232422%
Volume Distribution (VD):  0.638
Pgp-substrate:  14.610761642456055%

ADMET: Metabolism

CYP1A2-inhibitor:  0.976
CYP1A2-substrate:  0.408
CYP2C19-inhibitor:  0.832
CYP2C19-substrate:  0.346
CYP2C9-inhibitor:  0.77
CYP2C9-substrate:  0.159
CYP2D6-inhibitor:  0.377
CYP2D6-substrate:  0.139
CYP3A4-inhibitor:  0.546
CYP3A4-substrate:  0.2

ADMET: Excretion

Clearance (CL):  1.327
Half-life (T1/2):  0.547

ADMET: Toxicity

hERG Blockers:  0.001
Human Hepatotoxicity (H-HT):  0.879
Drug-inuced Liver Injury (DILI):  0.945
AMES Toxicity:  0.969
Rat Oral Acute Toxicity:  0.98
Maximum Recommended Daily Dose:  0.866
Skin Sensitization:  0.948
Carcinogencity:  0.821
Eye Corrosion:  0.931
Eye Irritation:  0.955
Respiratory Toxicity:  0.921

Download Data

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

  Natural Product: NPC146583

Natural Product ID:  NPC146583
Common Name*:   [(1R)-1-[(5Z)-4-Bromo-5-(Iodomethylidene)-2-Oxofuran-3-Yl]Butyl] Acetate
IUPAC Name:   [(1R)-1-[(5Z)-4-bromo-5-(iodomethylidene)-2-oxofuran-3-yl]butyl] acetate
Synonyms:  
Standard InCHIKey:  PQGNPRSFFPSLLF-BESBCXERSA-N
Standard InCHI:  InChI=1S/C11H12BrIO4/c1-3-4-7(16-6(2)14)9-10(12)8(5-13)17-11(9)15/h5,7H,3-4H2,1-2H3/b8-5-/t7-/m1/s1
SMILES:  CCC[C@H](C1=C(Br)/C(=C/I)/OC1=O)OC(=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL496439
PubChem CID:   21729104
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
NPO14524 Delisea pulchra Species Bonnemaisoniaceae Eukaryota n.a. n.a. n.a. PMID[16933872]
NPO14524 Delisea pulchra Species Bonnemaisoniaceae 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
NPT1034 Cell Line Lu1 Homo sapiens ED50 = 1.5 ug ml-1 PMID[449029]
NPT91 Cell Line KB Homo sapiens ED50 = 0.1 ug ml-1 PMID[449029]
NPT91 Cell Line KB Homo sapiens ED50 = 3.6 ug ml-1 PMID[449029]
NPT91 Cell Line KB Homo sapiens ED50 = 0.2 ug ml-1 PMID[449029]
NPT858 Cell Line LNCaP Homo sapiens ED50 = 2.0 ug ml-1 PMID[449029]
NPT133 Cell Line ZR-75-1 Homo sapiens ED50 < 0.1 ug ml-1 PMID[449029]
NPT459 Individual Protein Human immunodeficiency virus type 1 reverse transcriptase Human immunodeficiency virus 1 IC50 = 700000.0 nM PMID[449029]
NPT3085 Organism Penicillium oxalicum Penicillium oxalicum IZ = 17.0 mm PMID[449029]
NPT3085 Organism Penicillium oxalicum Penicillium oxalicum IZ = 21.0 mm PMID[449029]
NPT3085 Organism Penicillium oxalicum Penicillium oxalicum IZ = 9.0 mm PMID[449029]
NPT3085 Organism Penicillium oxalicum Penicillium oxalicum IZ = 6.0 mm PMID[449029]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 4.6 ug.mL-1 PMID[449029]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 > 10.0 ug.mL-1 PMID[449029]
NPT2 Others Unspecified Ratio IC50 < 1.0 n.a. PMID[449029]

☑ 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 NPC146583 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
0.9275 High Similarity NPC162571
0.9275 High Similarity NPC112983
0.9265 High Similarity NPC494
0.9167 High Similarity NPC24827
0.9167 High Similarity NPC228902
0.875 High Similarity NPC188354
0.8514 High Similarity NPC225022
0.8514 High Similarity NPC238554
0.8493 Intermediate Similarity NPC177030
0.8333 Intermediate Similarity NPC475113
0.8333 Intermediate Similarity NPC299932
0.8289 Intermediate Similarity NPC102065
0.8289 Intermediate Similarity NPC85743
0.8261 Intermediate Similarity NPC53136
0.8261 Intermediate Similarity NPC173409
0.8235 Intermediate Similarity NPC217537
0.8219 Intermediate Similarity NPC269103
0.8219 Intermediate Similarity NPC124072
0.8182 Intermediate Similarity NPC199134
0.8182 Intermediate Similarity NPC286816
0.7662 Intermediate Similarity NPC329826
0.7662 Intermediate Similarity NPC469414
0.75 Intermediate Similarity NPC133098
0.7397 Intermediate Similarity NPC475110
0.725 Intermediate Similarity NPC68156
0.7179 Intermediate Similarity NPC144419
0.7162 Intermediate Similarity NPC476589
0.7067 Intermediate Similarity NPC248125
0.6933 Remote Similarity NPC131174
0.6883 Remote Similarity NPC218477
0.6835 Remote Similarity NPC84038
0.6757 Remote Similarity NPC151648
0.6757 Remote Similarity NPC15193
0.6753 Remote Similarity NPC203335
0.675 Remote Similarity NPC474705
0.6711 Remote Similarity NPC182794
0.6711 Remote Similarity NPC133904
0.6667 Remote Similarity NPC238223
0.6667 Remote Similarity NPC474823
0.6667 Remote Similarity NPC474758
0.6667 Remote Similarity NPC287705
0.6628 Remote Similarity NPC8161
0.6627 Remote Similarity NPC10572
0.6625 Remote Similarity NPC186531
0.6588 Remote Similarity NPC47653
0.6585 Remote Similarity NPC478196
0.6585 Remote Similarity NPC478192
0.6585 Remote Similarity NPC478195
0.6585 Remote Similarity NPC478194
0.6585 Remote Similarity NPC478191
0.6585 Remote Similarity NPC478193
0.6585 Remote Similarity NPC161038
0.6582 Remote Similarity NPC475004
0.6552 Remote Similarity NPC475947
0.6548 Remote Similarity NPC475699
0.6543 Remote Similarity NPC287878
0.6538 Remote Similarity NPC132286
0.6522 Remote Similarity NPC6099
0.6522 Remote Similarity NPC114345
0.6522 Remote Similarity NPC327760
0.6522 Remote Similarity NPC303230
0.6512 Remote Similarity NPC42470
0.6506 Remote Similarity NPC123360
0.6506 Remote Similarity NPC271986
0.6486 Remote Similarity NPC286189
0.6486 Remote Similarity NPC133600
0.6471 Remote Similarity NPC178277
0.6471 Remote Similarity NPC473981
0.6471 Remote Similarity NPC473980
0.6463 Remote Similarity NPC117746
0.6463 Remote Similarity NPC294434
0.6463 Remote Similarity NPC476355
0.6463 Remote Similarity NPC15499
0.6463 Remote Similarity NPC259599
0.6456 Remote Similarity NPC280374
0.6456 Remote Similarity NPC477117
0.6447 Remote Similarity NPC179087
0.6447 Remote Similarity NPC132243
0.6447 Remote Similarity NPC210303
0.6447 Remote Similarity NPC44343
0.6447 Remote Similarity NPC473737
0.6447 Remote Similarity NPC68110
0.6437 Remote Similarity NPC26624
0.6429 Remote Similarity NPC275530
0.6429 Remote Similarity NPC57744
0.641 Remote Similarity NPC37382
0.6404 Remote Similarity NPC281172
0.6404 Remote Similarity NPC130030
0.6386 Remote Similarity NPC329852
0.6386 Remote Similarity NPC260396
0.6375 Remote Similarity NPC88877
0.6375 Remote Similarity NPC476591
0.6375 Remote Similarity NPC473277
0.6353 Remote Similarity NPC128276
0.6333 Remote Similarity NPC469483
0.6329 Remote Similarity NPC194871
0.6322 Remote Similarity NPC471325
0.6322 Remote Similarity NPC275507
0.631 Remote Similarity NPC51391
0.631 Remote Similarity NPC4492
0.6304 Remote Similarity NPC95364
0.6304 Remote Similarity NPC142159
0.6282 Remote Similarity NPC470123
0.6282 Remote Similarity NPC282760
0.6282 Remote Similarity NPC220766
0.6279 Remote Similarity NPC270126
0.6279 Remote Similarity NPC265980
0.6279 Remote Similarity NPC150646
0.6279 Remote Similarity NPC99651
0.6279 Remote Similarity NPC63326
0.6279 Remote Similarity NPC471299
0.6265 Remote Similarity NPC470686
0.6265 Remote Similarity NPC140287
0.625 Remote Similarity NPC470256
0.625 Remote Similarity NPC475690
0.625 Remote Similarity NPC276290
0.625 Remote Similarity NPC470032
0.6237 Remote Similarity NPC475879
0.6235 Remote Similarity NPC171204
0.6235 Remote Similarity NPC97516
0.6235 Remote Similarity NPC473825
0.6235 Remote Similarity NPC141789
0.6235 Remote Similarity NPC476028
0.6235 Remote Similarity NPC474760
0.6234 Remote Similarity NPC474774
0.6222 Remote Similarity NPC470755
0.622 Remote Similarity NPC293114
0.622 Remote Similarity NPC163003
0.6207 Remote Similarity NPC223904
0.6207 Remote Similarity NPC474510
0.6207 Remote Similarity NPC281132
0.6203 Remote Similarity NPC191233
0.6196 Remote Similarity NPC469653
0.6196 Remote Similarity NPC475902
0.6196 Remote Similarity NPC469631
0.6196 Remote Similarity NPC475906
0.6196 Remote Similarity NPC469628
0.6196 Remote Similarity NPC260343
0.6196 Remote Similarity NPC471047
0.6184 Remote Similarity NPC79756
0.6184 Remote Similarity NPC309408
0.618 Remote Similarity NPC16488
0.618 Remote Similarity NPC475989
0.6173 Remote Similarity NPC470693
0.6173 Remote Similarity NPC232812
0.6173 Remote Similarity NPC107130
0.6173 Remote Similarity NPC236208
0.617 Remote Similarity NPC166110
0.617 Remote Similarity NPC32944
0.617 Remote Similarity NPC193396
0.6164 Remote Similarity NPC478117
0.6163 Remote Similarity NPC93763
0.6163 Remote Similarity NPC182292
0.6163 Remote Similarity NPC299235
0.6163 Remote Similarity NPC253749
0.6163 Remote Similarity NPC315765
0.6163 Remote Similarity NPC264391
0.6163 Remote Similarity NPC108816
0.6154 Remote Similarity NPC261721
0.6145 Remote Similarity NPC295633
0.6145 Remote Similarity NPC58956
0.6145 Remote Similarity NPC269206
0.6136 Remote Similarity NPC297440
0.6129 Remote Similarity NPC225283
0.6129 Remote Similarity NPC64913
0.6129 Remote Similarity NPC242877
0.6125 Remote Similarity NPC472266
0.6125 Remote Similarity NPC225272
0.6118 Remote Similarity NPC16279
0.6118 Remote Similarity NPC205615
0.6118 Remote Similarity NPC301207
0.6118 Remote Similarity NPC256640
0.6111 Remote Similarity NPC41856
0.6111 Remote Similarity NPC163093
0.6111 Remote Similarity NPC163615
0.6111 Remote Similarity NPC158756
0.6111 Remote Similarity NPC38569
0.6105 Remote Similarity NPC248193
0.6098 Remote Similarity NPC472017
0.6098 Remote Similarity NPC64234
0.6098 Remote Similarity NPC67183
0.6098 Remote Similarity NPC37929
0.6098 Remote Similarity NPC315285
0.6098 Remote Similarity NPC69462
0.6092 Remote Similarity NPC472965
0.6092 Remote Similarity NPC63649
0.6092 Remote Similarity NPC264227
0.6092 Remote Similarity NPC271632
0.6081 Remote Similarity NPC86948
0.6071 Remote Similarity NPC474551
0.6071 Remote Similarity NPC48641
0.6071 Remote Similarity NPC227396
0.6071 Remote Similarity NPC114727
0.6071 Remote Similarity NPC476590
0.6067 Remote Similarity NPC473712
0.6067 Remote Similarity NPC473780
0.6067 Remote Similarity NPC329829
0.6067 Remote Similarity NPC180363
0.6067 Remote Similarity NPC475046
0.6067 Remote Similarity NPC11383

  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 NPC146583 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
0.6437 Remote Similarity NPD5209 Approved
0.5875 Remote Similarity NPD2685 Clinical (unspecified phase)
0.5833 Remote Similarity NPD6927 Phase 3
0.5714 Remote Similarity NPD4752 Clinical (unspecified phase)
0.5682 Remote Similarity NPD4756 Discovery
0.5632 Remote Similarity NPD8039 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