Structure

Physi-Chem Properties

Molecular Weight:  475.85
Volume:  301.444
LogP:  3.301
LogD:  2.058
LogS:  -4.476
# Rotatable Bonds:  7
TPSA:  61.83
# H-Bond Aceptor:  5
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.432
Synthetic Accessibility Score:  4.378
Fsp3:  0.667
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.5
MDCK Permeability:  5.397207860369235e-05
Pgp-inhibitor:  0.998
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.494
20% Bioavailability (F20%):  0.966
30% Bioavailability (F30%):  0.995

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.696
Plasma Protein Binding (PPB):  92.64775085449219%
Volume Distribution (VD):  1.691
Pgp-substrate:  16.488569259643555%

ADMET: Metabolism

CYP1A2-inhibitor:  0.758
CYP1A2-substrate:  0.832
CYP2C19-inhibitor:  0.718
CYP2C19-substrate:  0.847
CYP2C9-inhibitor:  0.938
CYP2C9-substrate:  0.04
CYP2D6-inhibitor:  0.005
CYP2D6-substrate:  0.122
CYP3A4-inhibitor:  0.583
CYP3A4-substrate:  0.898

ADMET: Excretion

Clearance (CL):  2.016
Half-life (T1/2):  0.249

ADMET: Toxicity

hERG Blockers:  0.019
Human Hepatotoxicity (H-HT):  0.176
Drug-inuced Liver Injury (DILI):  0.965
AMES Toxicity:  0.982
Rat Oral Acute Toxicity:  0.711
Maximum Recommended Daily Dose:  0.283
Skin Sensitization:  0.922
Carcinogencity:  0.78
Eye Corrosion:  0.951
Eye Irritation:  0.225
Respiratory Toxicity:  0.967

Download Data

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

  Natural Product: NPC269103

Natural Product ID:  NPC269103
Common Name*:   [(1R)-1-[(5S)-4-Bromo-5-(Dibromomethyl)-5-Methoxy-2-Oxofuran-3-Yl]Butyl] Acetate
IUPAC Name:   [(1R)-1-[(5S)-4-bromo-5-(dibromomethyl)-5-methoxy-2-oxofuran-3-yl]butyl] acetate
Synonyms:  
Standard InCHIKey:  MSGJXJIOEUCWTA-KRTXAFLBSA-N
Standard InCHI:  InChI=1S/C12H15Br3O5/c1-4-5-7(19-6(2)16)8-9(13)12(18-3,11(14)15)20-10(8)17/h7,11H,4-5H2,1-3H3/t7-,12+/m1/s1
SMILES:  CCC[C@H](C1=C([C@](C(Br)Br)(OC)OC1=O)Br)OC(=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL498427
PubChem CID:   21773482
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000254] Ethers
          • [CHEMONTID:0001656] Acetals
            • [CHEMONTID:0004472] Ketals

*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 > 20.0 ug ml-1 PMID[495434]
NPT91 Cell Line KB Homo sapiens ED50 = 4.1 ug ml-1 PMID[495434]
NPT91 Cell Line KB Homo sapiens ED50 = 3.9 ug ml-1 PMID[495434]
NPT91 Cell Line KB Homo sapiens ED50 = 6.2 ug ml-1 PMID[495434]
NPT858 Cell Line LNCaP Homo sapiens ED50 = 3.6 ug ml-1 PMID[495434]
NPT133 Cell Line ZR-75-1 Homo sapiens ED50 = 2.8 ug ml-1 PMID[495434]
NPT3085 Organism Penicillium oxalicum Penicillium oxalicum IZ = 16.0 mm PMID[495434]
NPT3085 Organism Penicillium oxalicum Penicillium oxalicum IZ = 14.0 mm PMID[495434]
NPT3085 Organism Penicillium oxalicum Penicillium oxalicum IZ = 6.0 mm PMID[495434]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 5.0 ug.mL-1 PMID[495434]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 > 10.0 ug.mL-1 PMID[495434]
NPT2 Others Unspecified Ratio IC50 = 1.0 n.a. PMID[495434]
NPT2 Others Unspecified Activity = 22.7 % PMID[495434]

☑ 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 NPC269103 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 NPC124072
0.9552 High Similarity NPC299932
0.9552 High Similarity NPC475113
0.9143 High Similarity NPC188354
0.9091 High Similarity NPC475110
0.8857 High Similarity NPC112983
0.8857 High Similarity NPC162571
0.8841 High Similarity NPC494
0.8649 High Similarity NPC85743
0.8649 High Similarity NPC102065
0.8219 Intermediate Similarity NPC146583
0.8133 Intermediate Similarity NPC225022
0.8133 Intermediate Similarity NPC238554
0.8108 Intermediate Similarity NPC177030
0.7857 Intermediate Similarity NPC173409
0.7857 Intermediate Similarity NPC53136
0.7826 Intermediate Similarity NPC217537
0.7564 Intermediate Similarity NPC24827
0.7564 Intermediate Similarity NPC228902
0.7375 Intermediate Similarity NPC286816
0.7375 Intermediate Similarity NPC199134
0.7273 Intermediate Similarity NPC144419
0.7125 Intermediate Similarity NPC10572
0.6933 Remote Similarity NPC248125
0.6875 Remote Similarity NPC329826
0.6875 Remote Similarity NPC469414
0.6753 Remote Similarity NPC218477
0.6753 Remote Similarity NPC470032
0.6709 Remote Similarity NPC84038
0.6709 Remote Similarity NPC133098
0.6667 Remote Similarity NPC47653
0.6625 Remote Similarity NPC474705
0.6623 Remote Similarity NPC203335
0.6622 Remote Similarity NPC151648
0.6585 Remote Similarity NPC271986
0.6552 Remote Similarity NPC41856
0.6543 Remote Similarity NPC474758
0.6538 Remote Similarity NPC280374
0.6512 Remote Similarity NPC11383
0.6512 Remote Similarity NPC310450
0.6512 Remote Similarity NPC474959
0.6512 Remote Similarity NPC475046
0.6506 Remote Similarity NPC68156
0.65 Remote Similarity NPC186531
0.6437 Remote Similarity NPC284472
0.6437 Remote Similarity NPC475947
0.6437 Remote Similarity NPC286770
0.6437 Remote Similarity NPC229799
0.6429 Remote Similarity NPC475699
0.6429 Remote Similarity NPC473784
0.6386 Remote Similarity NPC123360
0.6364 Remote Similarity NPC131174
0.6364 Remote Similarity NPC476589
0.6353 Remote Similarity NPC473981
0.6353 Remote Similarity NPC178277
0.6353 Remote Similarity NPC473980
0.6351 Remote Similarity NPC286189
0.6341 Remote Similarity NPC259599
0.6341 Remote Similarity NPC476355
0.6341 Remote Similarity NPC15499
0.6341 Remote Similarity NPC117746
0.6341 Remote Similarity NPC294434
0.6322 Remote Similarity NPC8161
0.6316 Remote Similarity NPC68110
0.631 Remote Similarity NPC57744
0.6277 Remote Similarity NPC471496
0.6265 Remote Similarity NPC329852
0.625 Remote Similarity NPC476591
0.625 Remote Similarity NPC88877
0.6235 Remote Similarity NPC128276
0.6222 Remote Similarity NPC469483
0.6211 Remote Similarity NPC473334
0.6207 Remote Similarity NPC275507
0.6207 Remote Similarity NPC471325
0.6203 Remote Similarity NPC194871
0.6163 Remote Similarity NPC150646
0.6163 Remote Similarity NPC270126
0.6163 Remote Similarity NPC471299
0.6163 Remote Similarity NPC99651
0.6154 Remote Similarity NPC282760
0.6154 Remote Similarity NPC182794
0.6154 Remote Similarity NPC133904
0.6154 Remote Similarity NPC470123
0.6146 Remote Similarity NPC240673
0.6146 Remote Similarity NPC17578
0.6145 Remote Similarity NPC140287
0.6136 Remote Similarity NPC475690
0.6129 Remote Similarity NPC475879
0.6125 Remote Similarity NPC276290
0.6125 Remote Similarity NPC470256
0.6125 Remote Similarity NPC474823
0.6118 Remote Similarity NPC97516
0.6118 Remote Similarity NPC171204
0.6118 Remote Similarity NPC476028
0.6118 Remote Similarity NPC141789
0.6118 Remote Similarity NPC474760
0.6111 Remote Similarity NPC469570
0.6111 Remote Similarity NPC48210
0.6111 Remote Similarity NPC470755
0.6105 Remote Similarity NPC475832
0.6105 Remote Similarity NPC475927
0.6105 Remote Similarity NPC474555
0.6104 Remote Similarity NPC474774
0.6098 Remote Similarity NPC163003
0.6092 Remote Similarity NPC223904
0.6092 Remote Similarity NPC281132
0.6087 Remote Similarity NPC471047
0.6087 Remote Similarity NPC475906
0.6087 Remote Similarity NPC469653
0.6087 Remote Similarity NPC475902
0.6087 Remote Similarity NPC469631
0.6087 Remote Similarity NPC469628
0.6076 Remote Similarity NPC284447
0.6071 Remote Similarity NPC161038
0.6053 Remote Similarity NPC79756
0.6049 Remote Similarity NPC107130
0.6049 Remote Similarity NPC475004
0.6047 Remote Similarity NPC299235
0.6047 Remote Similarity NPC253749
0.6047 Remote Similarity NPC93763
0.6047 Remote Similarity NPC108816
0.6044 Remote Similarity NPC261721
0.6027 Remote Similarity NPC49028
0.6024 Remote Similarity NPC58956
0.6024 Remote Similarity NPC295633
0.6024 Remote Similarity NPC269206
0.6024 Remote Similarity NPC287878
0.6023 Remote Similarity NPC297440
0.6023 Remote Similarity NPC42470
0.6023 Remote Similarity NPC282293
0.6022 Remote Similarity NPC64913
0.6022 Remote Similarity NPC242877
0.6 Remote Similarity NPC158756
0.6 Remote Similarity NPC256640
0.6 Remote Similarity NPC38569
0.6 Remote Similarity NPC205615
0.6 Remote Similarity NPC16279
0.6 Remote Similarity NPC163615
0.6 Remote Similarity NPC472266
0.6 Remote Similarity NPC163093
0.6 Remote Similarity NPC71626
0.5977 Remote Similarity NPC265980
0.5977 Remote Similarity NPC63326
0.5976 Remote Similarity NPC69462
0.5976 Remote Similarity NPC472017
0.5976 Remote Similarity NPC67183
0.5974 Remote Similarity NPC15193
0.5957 Remote Similarity NPC474098
0.5957 Remote Similarity NPC80875
0.5957 Remote Similarity NPC475995
0.5955 Remote Similarity NPC471296
0.5955 Remote Similarity NPC473529
0.5955 Remote Similarity NPC11332
0.5955 Remote Similarity NPC73310
0.5955 Remote Similarity NPC94875
0.5955 Remote Similarity NPC173609
0.5955 Remote Similarity NPC473780
0.5955 Remote Similarity NPC180363
0.5955 Remote Similarity NPC145914
0.5955 Remote Similarity NPC131002
0.5955 Remote Similarity NPC35556
0.5955 Remote Similarity NPC475159
0.5955 Remote Similarity NPC473712
0.5955 Remote Similarity NPC65930
0.5955 Remote Similarity NPC85772
0.5955 Remote Similarity NPC329829
0.5952 Remote Similarity NPC476590
0.5952 Remote Similarity NPC474551
0.5952 Remote Similarity NPC48641
0.5952 Remote Similarity NPC114727
0.5946 Remote Similarity NPC245002
0.5938 Remote Similarity NPC474554
0.5934 Remote Similarity NPC477014
0.5934 Remote Similarity NPC470124
0.5934 Remote Similarity NPC477013
0.5934 Remote Similarity NPC155873
0.5934 Remote Similarity NPC471567
0.5934 Remote Similarity NPC473353
0.5934 Remote Similarity NPC120398
0.593 Remote Similarity NPC187568
0.593 Remote Similarity NPC275530
0.593 Remote Similarity NPC41780
0.5926 Remote Similarity NPC238223
0.5926 Remote Similarity NPC287705
0.5918 Remote Similarity NPC471462
0.5918 Remote Similarity NPC475709
0.5914 Remote Similarity NPC475819
0.5914 Remote Similarity NPC476805
0.5904 Remote Similarity NPC129665
0.5897 Remote Similarity NPC179087
0.5897 Remote Similarity NPC217940
0.5897 Remote Similarity NPC44343
0.5897 Remote Similarity NPC210303
0.5897 Remote Similarity NPC474658
0.5897 Remote Similarity NPC473737
0.5895 Remote Similarity NPC6099
0.5895 Remote Similarity NPC327760
0.5895 Remote Similarity NPC114345
0.5895 Remote Similarity NPC470520
0.5895 Remote Similarity NPC473707

  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 NPC269103 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
0.5955 Remote Similarity NPD5209 Approved
0.575 Remote Similarity NPD2685 Clinical (unspecified phase)
0.5694 Remote Similarity NPD6927 Phase 3
0.5604 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