Structure

Physi-Chem Properties

Molecular Weight:  443.82
Volume:  272.722
LogP:  3.913
LogD:  2.028
LogS:  -4.202
# Rotatable Bonds:  5
TPSA:  52.6
# H-Bond Aceptor:  4
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.615
Synthetic Accessibility Score:  3.957
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:  -4.48
MDCK Permeability:  2.656575270520989e-05
Pgp-inhibitor:  0.999
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.184
20% Bioavailability (F20%):  0.981
30% Bioavailability (F30%):  0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.448
Plasma Protein Binding (PPB):  97.83753204345703%
Volume Distribution (VD):  1.065
Pgp-substrate:  8.54712200164795%

ADMET: Metabolism

CYP1A2-inhibitor:  0.979
CYP1A2-substrate:  0.151
CYP2C19-inhibitor:  0.742
CYP2C19-substrate:  0.291
CYP2C9-inhibitor:  0.913
CYP2C9-substrate:  0.176
CYP2D6-inhibitor:  0.196
CYP2D6-substrate:  0.098
CYP3A4-inhibitor:  0.487
CYP3A4-substrate:  0.221

ADMET: Excretion

Clearance (CL):  0.981
Half-life (T1/2):  0.341

ADMET: Toxicity

hERG Blockers:  0.004
Human Hepatotoxicity (H-HT):  0.926
Drug-inuced Liver Injury (DILI):  0.928
AMES Toxicity:  0.976
Rat Oral Acute Toxicity:  0.627
Maximum Recommended Daily Dose:  0.709
Skin Sensitization:  0.965
Carcinogencity:  0.671
Eye Corrosion:  0.963
Eye Irritation:  0.965
Respiratory Toxicity:  0.93

Download Data

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

  Natural Product: NPC494

Natural Product ID:  NPC494
Common Name*:   [(1R)-1-[4-Bromo-5-(Dibromomethylidene)-2-Oxofuran-3-Yl]Butyl] Acetate
IUPAC Name:   [(1R)-1-[4-bromo-5-(dibromomethylidene)-2-oxofuran-3-yl]butyl] acetate
Synonyms:  
Standard InCHIKey:  GKLOGZLMFMQARH-ZCFIWIBFSA-N
Standard InCHI:  InChI=1S/C11H11Br3O4/c1-3-4-6(17-5(2)15)7-8(12)9(10(13)14)18-11(7)16/h6H,3-4H2,1-2H3/t6-/m1/s1
SMILES:  CCC[C@H](C1=C(C(=C(Br)Br)OC1=O)Br)OC(=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL495662
PubChem CID:   21729105
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 = 1.1 ug ml-1 PMID[522983]
NPT91 Cell Line KB Homo sapiens ED50 = 0.3 ug ml-1 PMID[522983]
NPT91 Cell Line KB Homo sapiens ED50 = 0.5 ug ml-1 PMID[522983]
NPT91 Cell Line KB Homo sapiens ED50 = 3.5 ug ml-1 PMID[522983]
NPT858 Cell Line LNCaP Homo sapiens ED50 = 2.1 ug ml-1 PMID[522983]
NPT133 Cell Line ZR-75-1 Homo sapiens ED50 < 0.1 ug ml-1 PMID[522983]
NPT459 Individual Protein Human immunodeficiency virus type 1 reverse transcriptase Human immunodeficiency virus 1 IC50 = 700000.0 nM PMID[522983]
NPT3085 Organism Penicillium oxalicum Penicillium oxalicum IZ = 12.0 mm PMID[522983]
NPT3085 Organism Penicillium oxalicum Penicillium oxalicum IZ = 14.0 mm PMID[522983]
NPT3085 Organism Penicillium oxalicum Penicillium oxalicum IZ = 10.0 mm PMID[522983]
NPT3085 Organism Penicillium oxalicum Penicillium oxalicum IZ = 6.0 mm PMID[522983]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 2.2 ug.mL-1 PMID[522983]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 9.1 ug.mL-1 PMID[522983]
NPT2 Others Unspecified Ratio IC50 < 1.0 n.a. PMID[522983]
NPT2 Others Unspecified Activity = 1.9 % PMID[522983]
NPT3085 Organism Penicillium oxalicum Penicillium oxalicum IZ = 3.0 mm PMID[522983]

☑ 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 NPC494 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
0.9697 High Similarity NPC112983
0.9697 High Similarity NPC162571
0.9265 High Similarity NPC146583
0.913 High Similarity NPC177030
0.8906 High Similarity NPC217537
0.8873 High Similarity NPC238554
0.8873 High Similarity NPC225022
0.8841 High Similarity NPC124072
0.8841 High Similarity NPC269103
0.8696 High Similarity NPC299932
0.8696 High Similarity NPC475113
0.8636 High Similarity NPC53136
0.8636 High Similarity NPC173409
0.8493 Intermediate Similarity NPC228902
0.8493 Intermediate Similarity NPC24827
0.8333 Intermediate Similarity NPC188354
0.8267 Intermediate Similarity NPC199134
0.8267 Intermediate Similarity NPC286816
0.7971 Intermediate Similarity NPC475110
0.7895 Intermediate Similarity NPC102065
0.7895 Intermediate Similarity NPC85743
0.7733 Intermediate Similarity NPC469414
0.7733 Intermediate Similarity NPC329826
0.7568 Intermediate Similarity NPC133098
0.7467 Intermediate Similarity NPC144419
0.7308 Intermediate Similarity NPC68156
0.7222 Intermediate Similarity NPC476589
0.7123 Intermediate Similarity NPC248125
0.6986 Remote Similarity NPC131174
0.6933 Remote Similarity NPC218477
0.6883 Remote Similarity NPC84038
0.6867 Remote Similarity NPC8161
0.6829 Remote Similarity NPC47653
0.6806 Remote Similarity NPC151648
0.6806 Remote Similarity NPC15193
0.68 Remote Similarity NPC203335
0.6795 Remote Similarity NPC474705
0.6757 Remote Similarity NPC133904
0.6757 Remote Similarity NPC182794
0.675 Remote Similarity NPC271986
0.6711 Remote Similarity NPC238223
0.6711 Remote Similarity NPC474823
0.6711 Remote Similarity NPC470032
0.6711 Remote Similarity NPC287705
0.6709 Remote Similarity NPC474758
0.6667 Remote Similarity NPC186531
0.6667 Remote Similarity NPC10572
0.6625 Remote Similarity NPC478193
0.6625 Remote Similarity NPC478192
0.6625 Remote Similarity NPC161038
0.6625 Remote Similarity NPC478196
0.6625 Remote Similarity NPC478191
0.6625 Remote Similarity NPC478195
0.6625 Remote Similarity NPC478194
0.6623 Remote Similarity NPC473277
0.6623 Remote Similarity NPC475004
0.6588 Remote Similarity NPC475947
0.6585 Remote Similarity NPC475699
0.6582 Remote Similarity NPC287878
0.6579 Remote Similarity NPC132286
0.6556 Remote Similarity NPC327760
0.6556 Remote Similarity NPC114345
0.6556 Remote Similarity NPC303230
0.6556 Remote Similarity NPC6099
0.6548 Remote Similarity NPC42470
0.6543 Remote Similarity NPC123360
0.6528 Remote Similarity NPC133600
0.6528 Remote Similarity NPC286189
0.6506 Remote Similarity NPC473981
0.6506 Remote Similarity NPC473980
0.6506 Remote Similarity NPC178277
0.65 Remote Similarity NPC15499
0.65 Remote Similarity NPC476355
0.65 Remote Similarity NPC117746
0.65 Remote Similarity NPC259599
0.65 Remote Similarity NPC294434
0.6494 Remote Similarity NPC477117
0.6494 Remote Similarity NPC280374
0.6486 Remote Similarity NPC473737
0.6486 Remote Similarity NPC179087
0.6486 Remote Similarity NPC132243
0.6486 Remote Similarity NPC210303
0.6486 Remote Similarity NPC68110
0.6486 Remote Similarity NPC44343
0.6463 Remote Similarity NPC57744
0.6463 Remote Similarity NPC275530
0.6447 Remote Similarity NPC37382
0.6437 Remote Similarity NPC281172
0.6437 Remote Similarity NPC130030
0.642 Remote Similarity NPC260396
0.642 Remote Similarity NPC329852
0.641 Remote Similarity NPC88877
0.641 Remote Similarity NPC476591
0.6386 Remote Similarity NPC128276
0.6386 Remote Similarity NPC315765
0.6377 Remote Similarity NPC473784
0.6364 Remote Similarity NPC469483
0.6364 Remote Similarity NPC194871
0.6353 Remote Similarity NPC471325
0.6353 Remote Similarity NPC275507
0.6333 Remote Similarity NPC95364
0.6333 Remote Similarity NPC142159
0.6316 Remote Similarity NPC470123
0.6316 Remote Similarity NPC220766
0.6316 Remote Similarity NPC282760
0.631 Remote Similarity NPC265980
0.631 Remote Similarity NPC471299
0.631 Remote Similarity NPC99651
0.631 Remote Similarity NPC150646
0.631 Remote Similarity NPC63326
0.631 Remote Similarity NPC270126
0.6296 Remote Similarity NPC140287
0.6296 Remote Similarity NPC470686
0.6282 Remote Similarity NPC470256
0.6282 Remote Similarity NPC276290
0.6279 Remote Similarity NPC475690
0.6267 Remote Similarity NPC474774
0.6265 Remote Similarity NPC474760
0.6265 Remote Similarity NPC476028
0.6265 Remote Similarity NPC141789
0.6265 Remote Similarity NPC473825
0.6265 Remote Similarity NPC171204
0.6265 Remote Similarity NPC97516
0.6264 Remote Similarity NPC475879
0.625 Remote Similarity NPC293114
0.625 Remote Similarity NPC470755
0.625 Remote Similarity NPC163003
0.6235 Remote Similarity NPC223904
0.6235 Remote Similarity NPC281132
0.6235 Remote Similarity NPC474510
0.6234 Remote Similarity NPC191233
0.6222 Remote Similarity NPC469653
0.6222 Remote Similarity NPC260343
0.6222 Remote Similarity NPC475906
0.6222 Remote Similarity NPC475902
0.6222 Remote Similarity NPC469631
0.6222 Remote Similarity NPC471047
0.6222 Remote Similarity NPC469628
0.6216 Remote Similarity NPC309408
0.6216 Remote Similarity NPC79756
0.6207 Remote Similarity NPC16488
0.6207 Remote Similarity NPC475989
0.6203 Remote Similarity NPC232812
0.6203 Remote Similarity NPC236208
0.6203 Remote Similarity NPC470693
0.6203 Remote Similarity NPC107130
0.6197 Remote Similarity NPC49028
0.6197 Remote Similarity NPC478117
0.6196 Remote Similarity NPC166110
0.6196 Remote Similarity NPC32944
0.6196 Remote Similarity NPC193396
0.619 Remote Similarity NPC253749
0.619 Remote Similarity NPC299235
0.619 Remote Similarity NPC108816
0.619 Remote Similarity NPC182292
0.619 Remote Similarity NPC264391
0.619 Remote Similarity NPC93763
0.6184 Remote Similarity NPC471460
0.618 Remote Similarity NPC261721
0.6173 Remote Similarity NPC58956
0.6173 Remote Similarity NPC269206
0.6173 Remote Similarity NPC295633
0.6163 Remote Similarity NPC282293
0.6163 Remote Similarity NPC297440
0.6154 Remote Similarity NPC472266
0.6154 Remote Similarity NPC64913
0.6154 Remote Similarity NPC225272
0.6154 Remote Similarity NPC242877
0.6154 Remote Similarity NPC225283
0.6145 Remote Similarity NPC205615
0.6145 Remote Similarity NPC16279
0.6145 Remote Similarity NPC301207
0.6145 Remote Similarity NPC256640
0.6136 Remote Similarity NPC163615
0.6136 Remote Similarity NPC158756
0.6136 Remote Similarity NPC38569
0.6136 Remote Similarity NPC41856
0.6136 Remote Similarity NPC163093
0.6129 Remote Similarity NPC248193
0.6125 Remote Similarity NPC64234
0.6125 Remote Similarity NPC472017
0.6125 Remote Similarity NPC315285
0.6125 Remote Similarity NPC67183
0.6125 Remote Similarity NPC37929
0.6125 Remote Similarity NPC69462
0.6118 Remote Similarity NPC264227
0.6118 Remote Similarity NPC271632
0.6118 Remote Similarity NPC472965
0.6118 Remote Similarity NPC63649
0.6111 Remote Similarity NPC86948
0.6098 Remote Similarity NPC114727
0.6098 Remote Similarity NPC227396
0.6098 Remote Similarity NPC476590
0.6098 Remote Similarity NPC48641
0.6098 Remote Similarity NPC474551
0.6092 Remote Similarity NPC329829
0.6092 Remote Similarity NPC131002
0.6092 Remote Similarity NPC35556
0.6092 Remote Similarity NPC73310
0.6092 Remote Similarity NPC145914

  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 NPC494 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
0.6471 Remote Similarity NPD5209 Approved
0.5897 Remote Similarity NPD2685 Clinical (unspecified phase)
0.5857 Remote Similarity NPD6927 Phase 3
0.573 Remote Similarity NPD4752 Clinical (unspecified phase)
0.5698 Remote Similarity NPD4756 Discovery
0.5647 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