Structure

Physi-Chem Properties

Molecular Weight:  320.03
Volume:  262.877
LogP:  2.394
LogD:  1.664
LogS:  -2.881
# Rotatable Bonds:  6
TPSA:  61.83
# H-Bond Aceptor:  5
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.727
Synthetic Accessibility Score:  4.001
Fsp3:  0.667
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -4.508
MDCK Permeability:  4.3432184611447155e-05
Pgp-inhibitor:  0.995
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.01
20% Bioavailability (F20%):  0.95
30% Bioavailability (F30%):  0.991

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.87
Plasma Protein Binding (PPB):  82.38227844238281%
Volume Distribution (VD):  1.186
Pgp-substrate:  29.1585750579834%

ADMET: Metabolism

CYP1A2-inhibitor:  0.695
CYP1A2-substrate:  0.476
CYP2C19-inhibitor:  0.62
CYP2C19-substrate:  0.839
CYP2C9-inhibitor:  0.352
CYP2C9-substrate:  0.062
CYP2D6-inhibitor:  0.011
CYP2D6-substrate:  0.146
CYP3A4-inhibitor:  0.206
CYP3A4-substrate:  0.511

ADMET: Excretion

Clearance (CL):  3.827
Half-life (T1/2):  0.817

ADMET: Toxicity

hERG Blockers:  0.008
Human Hepatotoxicity (H-HT):  0.176
Drug-inuced Liver Injury (DILI):  0.955
AMES Toxicity:  0.957
Rat Oral Acute Toxicity:  0.251
Maximum Recommended Daily Dose:  0.235
Skin Sensitization:  0.604
Carcinogencity:  0.858
Eye Corrosion:  0.519
Eye Irritation:  0.854
Respiratory Toxicity:  0.76

Download Data

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

  Natural Product: NPC299932

Natural Product ID:  NPC299932
Common Name*:   [(1R)-1-[(5R)-4-Bromo-5-Methoxy-5-Methyl-2-Oxofuran-3-Yl]Butyl] Acetate
IUPAC Name:   [(1R)-1-[(5R)-4-bromo-5-methoxy-5-methyl-2-oxofuran-3-yl]butyl] acetate
Synonyms:  
Standard InCHIKey:  KZVSYNZEHWQHJE-PRHODGIISA-N
Standard InCHI:  InChI=1S/C12H17BrO5/c1-5-6-8(17-7(2)14)9-10(13)12(3,16-4)18-11(9)15/h8H,5-6H2,1-4H3/t8-,12-/m1/s1
SMILES:  CCC[C@H](C1=C([C@](C)(OC)OC1=O)Br)OC(=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL511073
PubChem CID:   21773483
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[534514]
NPT91 Cell Line KB Homo sapiens ED50 = 3.9 ug ml-1 PMID[534514]
NPT91 Cell Line KB Homo sapiens ED50 = 5.6 ug ml-1 PMID[534514]
NPT91 Cell Line KB Homo sapiens ED50 = 4.7 ug ml-1 PMID[534514]
NPT858 Cell Line LNCaP Homo sapiens ED50 = 3.6 ug ml-1 PMID[534514]
NPT133 Cell Line ZR-75-1 Homo sapiens ED50 = 4.0 ug ml-1 PMID[534514]
NPT3085 Organism Penicillium oxalicum Penicillium oxalicum IZ = 16.0 mm PMID[534514]
NPT3085 Organism Penicillium oxalicum Penicillium oxalicum IZ = 12.0 mm PMID[534514]
NPT3085 Organism Penicillium oxalicum Penicillium oxalicum IZ = 8.0 mm PMID[534514]
NPT2 Others Unspecified Activity = 86.0 % PMID[534514]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum Activity > 50.0 % PMID[534514]

☑ 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 NPC299932 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 NPC475113
0.9559 High Similarity NPC188354
0.9552 High Similarity NPC269103
0.9552 High Similarity NPC124072
0.8767 High Similarity NPC85743
0.8767 High Similarity NPC102065
0.8696 High Similarity NPC494
0.8657 High Similarity NPC475110
0.8451 Intermediate Similarity NPC112983
0.8451 Intermediate Similarity NPC162571
0.8333 Intermediate Similarity NPC146583
0.7973 Intermediate Similarity NPC177030
0.7763 Intermediate Similarity NPC238554
0.7763 Intermediate Similarity NPC225022
0.7681 Intermediate Similarity NPC217537
0.7662 Intermediate Similarity NPC24827
0.7662 Intermediate Similarity NPC228902
0.76 Intermediate Similarity NPC144419
0.7468 Intermediate Similarity NPC286816
0.7468 Intermediate Similarity NPC199134
0.7465 Intermediate Similarity NPC173409
0.7465 Intermediate Similarity NPC53136
0.7436 Intermediate Similarity NPC10572
0.726 Intermediate Similarity NPC248125
0.7179 Intermediate Similarity NPC329826
0.7179 Intermediate Similarity NPC469414
0.7067 Intermediate Similarity NPC218477
0.7013 Intermediate Similarity NPC84038
0.6951 Remote Similarity NPC47653
0.6944 Remote Similarity NPC151648
0.6933 Remote Similarity NPC203335
0.6923 Remote Similarity NPC474705
0.6835 Remote Similarity NPC474758
0.6824 Remote Similarity NPC41856
0.6795 Remote Similarity NPC186531
0.6795 Remote Similarity NPC133098
0.679 Remote Similarity NPC68156
0.6786 Remote Similarity NPC475046
0.6786 Remote Similarity NPC11383
0.6786 Remote Similarity NPC474959
0.6786 Remote Similarity NPC310450
0.6706 Remote Similarity NPC286770
0.6706 Remote Similarity NPC284472
0.6706 Remote Similarity NPC229799
0.6706 Remote Similarity NPC475947
0.6667 Remote Similarity NPC271986
0.6667 Remote Similarity NPC123360
0.6667 Remote Similarity NPC286189
0.6627 Remote Similarity NPC473980
0.6627 Remote Similarity NPC178277
0.6627 Remote Similarity NPC473981
0.6625 Remote Similarity NPC476355
0.6625 Remote Similarity NPC117746
0.6625 Remote Similarity NPC15499
0.6625 Remote Similarity NPC259599
0.6625 Remote Similarity NPC294434
0.6623 Remote Similarity NPC280374
0.6623 Remote Similarity NPC470032
0.6622 Remote Similarity NPC68110
0.6585 Remote Similarity NPC57744
0.6543 Remote Similarity NPC329852
0.6538 Remote Similarity NPC476591
0.6538 Remote Similarity NPC88877
0.6522 Remote Similarity NPC471496
0.6506 Remote Similarity NPC475699
0.6506 Remote Similarity NPC128276
0.6494 Remote Similarity NPC194871
0.6477 Remote Similarity NPC469483
0.6471 Remote Similarity NPC275507
0.6471 Remote Similarity NPC471325
0.6452 Remote Similarity NPC473334
0.6447 Remote Similarity NPC133904
0.6447 Remote Similarity NPC282760
0.6447 Remote Similarity NPC131174
0.6447 Remote Similarity NPC476589
0.6447 Remote Similarity NPC182794
0.6429 Remote Similarity NPC270126
0.6429 Remote Similarity NPC150646
0.6429 Remote Similarity NPC471299
0.6429 Remote Similarity NPC99651
0.642 Remote Similarity NPC140287
0.641 Remote Similarity NPC474823
0.641 Remote Similarity NPC470256
0.641 Remote Similarity NPC276290
0.64 Remote Similarity NPC474774
0.6395 Remote Similarity NPC475690
0.6386 Remote Similarity NPC476028
0.6386 Remote Similarity NPC97516
0.6386 Remote Similarity NPC171204
0.6386 Remote Similarity NPC474760
0.6386 Remote Similarity NPC141789
0.6383 Remote Similarity NPC240673
0.6383 Remote Similarity NPC17578
0.6375 Remote Similarity NPC163003
0.6374 Remote Similarity NPC475879
0.6364 Remote Similarity NPC470755
0.6364 Remote Similarity NPC284447
0.6353 Remote Similarity NPC281132
0.6353 Remote Similarity NPC223904
0.6351 Remote Similarity NPC79756
0.6344 Remote Similarity NPC475927
0.6344 Remote Similarity NPC474555
0.6344 Remote Similarity NPC475832
0.6333 Remote Similarity NPC471047
0.6333 Remote Similarity NPC469653
0.6333 Remote Similarity NPC469628
0.6333 Remote Similarity NPC475906
0.6333 Remote Similarity NPC475902
0.6333 Remote Similarity NPC469631
0.6329 Remote Similarity NPC475004
0.6329 Remote Similarity NPC107130
0.631 Remote Similarity NPC253749
0.631 Remote Similarity NPC93763
0.631 Remote Similarity NPC299235
0.631 Remote Similarity NPC108816
0.6296 Remote Similarity NPC269206
0.6296 Remote Similarity NPC287878
0.6296 Remote Similarity NPC295633
0.6296 Remote Similarity NPC58956
0.6292 Remote Similarity NPC261721
0.6286 Remote Similarity NPC473784
0.6282 Remote Similarity NPC472266
0.6279 Remote Similarity NPC282293
0.6279 Remote Similarity NPC297440
0.6279 Remote Similarity NPC42470
0.6265 Remote Similarity NPC256640
0.6265 Remote Similarity NPC16279
0.6265 Remote Similarity NPC205615
0.6264 Remote Similarity NPC64913
0.6264 Remote Similarity NPC242877
0.625 Remote Similarity NPC245002
0.625 Remote Similarity NPC163093
0.625 Remote Similarity NPC71626
0.625 Remote Similarity NPC472017
0.625 Remote Similarity NPC38569
0.625 Remote Similarity NPC69462
0.625 Remote Similarity NPC163615
0.625 Remote Similarity NPC158756
0.625 Remote Similarity NPC67183
0.6235 Remote Similarity NPC63326
0.6235 Remote Similarity NPC265980
0.6234 Remote Similarity NPC470123
0.622 Remote Similarity NPC476590
0.622 Remote Similarity NPC114727
0.622 Remote Similarity NPC474551
0.6207 Remote Similarity NPC329829
0.6207 Remote Similarity NPC8161
0.6207 Remote Similarity NPC65930
0.6207 Remote Similarity NPC131002
0.6207 Remote Similarity NPC11332
0.6207 Remote Similarity NPC94875
0.6207 Remote Similarity NPC145914
0.6207 Remote Similarity NPC173609
0.6207 Remote Similarity NPC73310
0.6207 Remote Similarity NPC473780
0.6207 Remote Similarity NPC180363
0.6207 Remote Similarity NPC35556
0.6207 Remote Similarity NPC85772
0.6207 Remote Similarity NPC475159
0.6207 Remote Similarity NPC471296
0.6207 Remote Similarity NPC473529
0.6207 Remote Similarity NPC473712
0.6203 Remote Similarity NPC238223
0.6196 Remote Similarity NPC474098
0.6196 Remote Similarity NPC475995
0.6196 Remote Similarity NPC80875
0.619 Remote Similarity NPC41780
0.619 Remote Similarity NPC187568
0.6184 Remote Similarity NPC179087
0.6184 Remote Similarity NPC210303
0.6184 Remote Similarity NPC217940
0.6184 Remote Similarity NPC474658
0.6184 Remote Similarity NPC44343
0.618 Remote Similarity NPC477014
0.618 Remote Similarity NPC473353
0.618 Remote Similarity NPC471567
0.618 Remote Similarity NPC469570
0.618 Remote Similarity NPC155873
0.618 Remote Similarity NPC120398
0.618 Remote Similarity NPC477013
0.618 Remote Similarity NPC470124
0.618 Remote Similarity NPC48210
0.6176 Remote Similarity NPC135698
0.6173 Remote Similarity NPC129665
0.617 Remote Similarity NPC474554
0.6154 Remote Similarity NPC476805
0.6154 Remote Similarity NPC475819
0.6146 Remote Similarity NPC475709
0.6146 Remote Similarity NPC471462
0.6145 Remote Similarity NPC478193
0.6145 Remote Similarity NPC478191
0.6145 Remote Similarity NPC478195
0.6145 Remote Similarity NPC473948
0.6145 Remote Similarity NPC478194
0.6145 Remote Similarity NPC478196
0.6145 Remote Similarity NPC161038
0.6145 Remote Similarity NPC478192
0.6145 Remote Similarity NPC260396
0.6136 Remote Similarity NPC144415
0.6136 Remote Similarity NPC40746

  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 NPC299932 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
0.6207 Remote Similarity NPD5209 Approved
0.6026 Remote Similarity NPD2685 Clinical (unspecified phase)
0.6 Remote Similarity NPD6927 Phase 3
0.5843 Remote Similarity NPD4752 Clinical (unspecified phase)
0.5714 Remote Similarity NPD6400 Clinical (unspecified phase)
0.5652 Remote Similarity NPD1694 Approved
0.5612 Remote Similarity NPD1698 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