Structure

Physi-Chem Properties

Molecular Weight:  445.92
Volume:  288.154
LogP:  2.962
LogD:  1.679
LogS:  -3.563
# Rotatable Bonds:  7
TPSA:  61.83
# H-Bond Aceptor:  5
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.356
Synthetic Accessibility Score:  4.343
Fsp3:  0.667
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -4.512
MDCK Permeability:  3.46051856467966e-05
Pgp-inhibitor:  0.901
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.013
20% Bioavailability (F20%):  0.925
30% Bioavailability (F30%):  0.981

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.891
Plasma Protein Binding (PPB):  81.00084686279297%
Volume Distribution (VD):  1.082
Pgp-substrate:  28.670238494873047%

ADMET: Metabolism

CYP1A2-inhibitor:  0.797
CYP1A2-substrate:  0.653
CYP2C19-inhibitor:  0.684
CYP2C19-substrate:  0.824
CYP2C9-inhibitor:  0.542
CYP2C9-substrate:  0.065
CYP2D6-inhibitor:  0.035
CYP2D6-substrate:  0.202
CYP3A4-inhibitor:  0.402
CYP3A4-substrate:  0.547

ADMET: Excretion

Clearance (CL):  3.598
Half-life (T1/2):  0.83

ADMET: Toxicity

hERG Blockers:  0.015
Human Hepatotoxicity (H-HT):  0.493
Drug-inuced Liver Injury (DILI):  0.941
AMES Toxicity:  0.984
Rat Oral Acute Toxicity:  0.636
Maximum Recommended Daily Dose:  0.248
Skin Sensitization:  0.906
Carcinogencity:  0.628
Eye Corrosion:  0.905
Eye Irritation:  0.509
Respiratory Toxicity:  0.868

Download Data

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

  Natural Product: NPC188354

Natural Product ID:  NPC188354
Common Name*:   [(1R)-1-[(5R)-4-Bromo-5-(Iodomethyl)-5-Methoxy-2-Oxofuran-3-Yl]Butyl] Acetate
IUPAC Name:   [(1R)-1-[(5R)-4-bromo-5-(iodomethyl)-5-methoxy-2-oxofuran-3-yl]butyl] acetate
Synonyms:  
Standard InCHIKey:  JLDSXGUGUNGPOD-PELKAZGASA-N
Standard InCHI:  InChI=1S/C12H16BrIO5/c1-4-5-8(18-7(2)15)9-10(13)12(6-14,17-3)19-11(9)16/h8H,4-6H2,1-3H3/t8-,12+/m1/s1
SMILES:  CCC[C@H](C1=C(Br)[C@@](OC1=O)(CI)OC)OC(=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL501092
PubChem CID:   479936
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[558927]
NPT91 Cell Line KB Homo sapiens ED50 = 2.4 ug ml-1 PMID[558927]
NPT91 Cell Line KB Homo sapiens ED50 = 4.1 ug ml-1 PMID[558927]
NPT91 Cell Line KB Homo sapiens ED50 = 7.1 ug ml-1 PMID[558927]
NPT858 Cell Line LNCaP Homo sapiens ED50 = 12.9 ug ml-1 PMID[558927]
NPT133 Cell Line ZR-75-1 Homo sapiens ED50 = 7.9 ug ml-1 PMID[558927]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum Activity > 50.0 % PMID[558927]
NPT1513 Organism Mycobacterium avium Mycobacterium avium IC50 = 350000.0 nM PMID[558927]

☑ 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 NPC188354 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
0.9559 High Similarity NPC475113
0.9559 High Similarity NPC299932
0.9178 High Similarity NPC85743
0.9178 High Similarity NPC102065
0.9143 High Similarity NPC124072
0.9143 High Similarity NPC269103
0.875 High Similarity NPC146583
0.8333 Intermediate Similarity NPC494
0.8286 Intermediate Similarity NPC475110
0.8108 Intermediate Similarity NPC162571
0.8108 Intermediate Similarity NPC112983
0.8052 Intermediate Similarity NPC228902
0.8052 Intermediate Similarity NPC24827
0.7662 Intermediate Similarity NPC177030
0.7468 Intermediate Similarity NPC225022
0.7468 Intermediate Similarity NPC238554
0.7361 Intermediate Similarity NPC217537
0.7308 Intermediate Similarity NPC144419
0.7195 Intermediate Similarity NPC199134
0.7195 Intermediate Similarity NPC286816
0.7162 Intermediate Similarity NPC53136
0.7162 Intermediate Similarity NPC173409
0.716 Intermediate Similarity NPC10572
0.6974 Remote Similarity NPC248125
0.6914 Remote Similarity NPC329826
0.6914 Remote Similarity NPC469414
0.6795 Remote Similarity NPC218477
0.675 Remote Similarity NPC84038
0.6706 Remote Similarity NPC47653
0.6667 Remote Similarity NPC151648
0.6667 Remote Similarity NPC203335
0.6667 Remote Similarity NPC474705
0.6591 Remote Similarity NPC41856
0.6585 Remote Similarity NPC474758
0.6552 Remote Similarity NPC475046
0.6552 Remote Similarity NPC11383
0.6552 Remote Similarity NPC474959
0.6552 Remote Similarity NPC310450
0.6548 Remote Similarity NPC68156
0.6543 Remote Similarity NPC133098
0.6543 Remote Similarity NPC186531
0.6477 Remote Similarity NPC229799
0.6477 Remote Similarity NPC475947
0.6477 Remote Similarity NPC284472
0.6477 Remote Similarity NPC286770
0.6429 Remote Similarity NPC271986
0.6429 Remote Similarity NPC123360
0.64 Remote Similarity NPC286189
0.6395 Remote Similarity NPC473981
0.6395 Remote Similarity NPC178277
0.6395 Remote Similarity NPC473980
0.6386 Remote Similarity NPC15499
0.6386 Remote Similarity NPC294434
0.6386 Remote Similarity NPC259599
0.6386 Remote Similarity NPC476355
0.6386 Remote Similarity NPC117746
0.6375 Remote Similarity NPC470032
0.6375 Remote Similarity NPC280374
0.6364 Remote Similarity NPC26624
0.6364 Remote Similarity NPC68110
0.6353 Remote Similarity NPC57744
0.6316 Remote Similarity NPC471496
0.631 Remote Similarity NPC329852
0.6296 Remote Similarity NPC88877
0.6296 Remote Similarity NPC476591
0.6279 Remote Similarity NPC475699
0.6279 Remote Similarity NPC128276
0.6264 Remote Similarity NPC469483
0.625 Remote Similarity NPC194871
0.625 Remote Similarity NPC473334
0.625 Remote Similarity NPC275507
0.625 Remote Similarity NPC471325
0.6207 Remote Similarity NPC270126
0.6207 Remote Similarity NPC99651
0.6207 Remote Similarity NPC471299
0.6207 Remote Similarity NPC150646
0.6203 Remote Similarity NPC282760
0.6203 Remote Similarity NPC182794
0.6203 Remote Similarity NPC476589
0.6203 Remote Similarity NPC133904
0.6203 Remote Similarity NPC131174
0.619 Remote Similarity NPC140287
0.6186 Remote Similarity NPC17578
0.6186 Remote Similarity NPC240673
0.618 Remote Similarity NPC475690
0.6173 Remote Similarity NPC470256
0.6173 Remote Similarity NPC276290
0.6173 Remote Similarity NPC474823
0.617 Remote Similarity NPC475879
0.6163 Remote Similarity NPC141789
0.6163 Remote Similarity NPC474760
0.6163 Remote Similarity NPC476028
0.6163 Remote Similarity NPC171204
0.6163 Remote Similarity NPC97516
0.6154 Remote Similarity NPC470755
0.6154 Remote Similarity NPC474774
0.6146 Remote Similarity NPC475832
0.6146 Remote Similarity NPC474555
0.6146 Remote Similarity NPC475927
0.6145 Remote Similarity NPC163003
0.6136 Remote Similarity NPC281132
0.6136 Remote Similarity NPC223904
0.6129 Remote Similarity NPC471047
0.6129 Remote Similarity NPC469653
0.6129 Remote Similarity NPC469628
0.6129 Remote Similarity NPC475906
0.6129 Remote Similarity NPC469631
0.6129 Remote Similarity NPC475902
0.6125 Remote Similarity NPC284447
0.6104 Remote Similarity NPC79756
0.6098 Remote Similarity NPC107130
0.6098 Remote Similarity NPC475004
0.6092 Remote Similarity NPC93763
0.6092 Remote Similarity NPC299235
0.6092 Remote Similarity NPC108816
0.6092 Remote Similarity NPC253749
0.6087 Remote Similarity NPC261721
0.6071 Remote Similarity NPC287878
0.6071 Remote Similarity NPC58956
0.6071 Remote Similarity NPC295633
0.6071 Remote Similarity NPC269206
0.6067 Remote Similarity NPC42470
0.6067 Remote Similarity NPC282293
0.6067 Remote Similarity NPC297440
0.6064 Remote Similarity NPC64913
0.6064 Remote Similarity NPC242877
0.6049 Remote Similarity NPC472266
0.6047 Remote Similarity NPC256640
0.6047 Remote Similarity NPC205615
0.6047 Remote Similarity NPC16279
0.6044 Remote Similarity NPC38569
0.6044 Remote Similarity NPC158756
0.6044 Remote Similarity NPC71626
0.6044 Remote Similarity NPC163615
0.6044 Remote Similarity NPC163093
0.6027 Remote Similarity NPC473784
0.6024 Remote Similarity NPC69462
0.6024 Remote Similarity NPC472017
0.6024 Remote Similarity NPC67183
0.6023 Remote Similarity NPC265980
0.6023 Remote Similarity NPC63326
0.6 Remote Similarity NPC473529
0.6 Remote Similarity NPC8161
0.6 Remote Similarity NPC474551
0.6 Remote Similarity NPC73310
0.6 Remote Similarity NPC474098
0.6 Remote Similarity NPC80875
0.6 Remote Similarity NPC131002
0.6 Remote Similarity NPC473780
0.6 Remote Similarity NPC471296
0.6 Remote Similarity NPC35556
0.6 Remote Similarity NPC245002
0.6 Remote Similarity NPC173609
0.6 Remote Similarity NPC145914
0.6 Remote Similarity NPC470123
0.6 Remote Similarity NPC94875
0.6 Remote Similarity NPC65930
0.6 Remote Similarity NPC11332
0.6 Remote Similarity NPC476590
0.6 Remote Similarity NPC180363
0.6 Remote Similarity NPC475995
0.6 Remote Similarity NPC114727
0.6 Remote Similarity NPC85772
0.6 Remote Similarity NPC329829
0.6 Remote Similarity NPC475159
0.6 Remote Similarity NPC473712
0.5979 Remote Similarity NPC474554
0.5978 Remote Similarity NPC477013
0.5978 Remote Similarity NPC469570
0.5978 Remote Similarity NPC477014
0.5978 Remote Similarity NPC470124
0.5978 Remote Similarity NPC473353
0.5978 Remote Similarity NPC471567
0.5978 Remote Similarity NPC48210
0.5978 Remote Similarity NPC155873
0.5978 Remote Similarity NPC120398
0.5977 Remote Similarity NPC187568
0.5977 Remote Similarity NPC41780
0.5976 Remote Similarity NPC238223
0.596 Remote Similarity NPC475709
0.596 Remote Similarity NPC471462
0.5957 Remote Similarity NPC476805
0.5957 Remote Similarity NPC475819
0.5952 Remote Similarity NPC129665
0.5949 Remote Similarity NPC210303
0.5949 Remote Similarity NPC217940
0.5949 Remote Similarity NPC474658
0.5949 Remote Similarity NPC44343
0.5949 Remote Similarity NPC179087
0.5938 Remote Similarity NPC473707
0.5938 Remote Similarity NPC470520
0.5938 Remote Similarity NPC327760
0.5938 Remote Similarity NPC303230
0.5938 Remote Similarity NPC6099
0.5938 Remote Similarity NPC141831
0.5938 Remote Similarity NPC114345
0.5934 Remote Similarity NPC318468
0.5934 Remote Similarity NPC253801
0.5934 Remote Similarity NPC169575
0.5934 Remote Similarity NPC144415

  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 NPC188354 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
0.6 Remote Similarity NPD5209 Approved
0.5802 Remote Similarity NPD2685 Clinical (unspecified phase)
0.5753 Remote Similarity NPD6927 Phase 3
0.5652 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