Structure

Physi-Chem Properties

Molecular Weight:  323.9
Volume:  212.692
LogP:  2.741
LogD:  1.438
LogS:  -3.079
# Rotatable Bonds:  3
TPSA:  46.53
# H-Bond Aceptor:  3
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.811
Synthetic Accessibility Score:  3.921
Fsp3:  0.444
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:  -4.489
MDCK Permeability:  2.3998029064387083e-05
Pgp-inhibitor:  0.784
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.012
20% Bioavailability (F20%):  0.874
30% Bioavailability (F30%):  0.983

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.431
Plasma Protein Binding (PPB):  96.4527816772461%
Volume Distribution (VD):  0.543
Pgp-substrate:  11.15018081665039%

ADMET: Metabolism

CYP1A2-inhibitor:  0.925
CYP1A2-substrate:  0.652
CYP2C19-inhibitor:  0.524
CYP2C19-substrate:  0.406
CYP2C9-inhibitor:  0.394
CYP2C9-substrate:  0.419
CYP2D6-inhibitor:  0.255
CYP2D6-substrate:  0.131
CYP3A4-inhibitor:  0.275
CYP3A4-substrate:  0.174

ADMET: Excretion

Clearance (CL):  1.333
Half-life (T1/2):  0.285

ADMET: Toxicity

hERG Blockers:  0.002
Human Hepatotoxicity (H-HT):  0.917
Drug-inuced Liver Injury (DILI):  0.876
AMES Toxicity:  0.969
Rat Oral Acute Toxicity:  0.985
Maximum Recommended Daily Dose:  0.959
Skin Sensitization:  0.934
Carcinogencity:  0.89
Eye Corrosion:  0.98
Eye Irritation:  0.991
Respiratory Toxicity:  0.943

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

  Natural Product: NPC225022

Natural Product ID:  NPC225022
Common Name*:   (R,Z)-4-Bromo-5-(Bromomethylene)-3-(1-Hydroxybutyl)Furan-2(5H)-One
IUPAC Name:   (5Z)-4-bromo-5-(bromomethylidene)-3-[(1R)-1-hydroxybutyl]furan-2-one
Synonyms:  
Standard InCHIKey:  GWLDADMCKOCKLF-WEWOIACBSA-N
Standard InCHI:  InChI=1S/C9H10Br2O3/c1-2-3-5(12)7-8(11)6(4-10)14-9(7)13/h4-5,12H,2-3H2,1H3/b6-4-/t5-/m1/s1
SMILES:  CCC[C@H](C1=C(/C(=C/Br)/OC1=O)Br)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL501176
PubChem CID:   6475696
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 = 0.3 ug ml-1 PMID[573706]
NPT91 Cell Line KB Homo sapiens ED50 = 0.4 ug ml-1 PMID[573706]
NPT91 Cell Line KB Homo sapiens ED50 = 3.4 ug ml-1 PMID[573706]
NPT91 Cell Line KB Homo sapiens ED50 = 0.1 ug ml-1 PMID[573706]
NPT858 Cell Line LNCaP Homo sapiens ED50 = 0.2 ug ml-1 PMID[573706]
NPT133 Cell Line ZR-75-1 Homo sapiens ED50 < 0.1 ug ml-1 PMID[573706]
NPT3085 Organism Penicillium oxalicum Penicillium oxalicum IZ = 27.0 mm PMID[573706]
NPT3085 Organism Penicillium oxalicum Penicillium oxalicum IZ = 26.0 mm PMID[573706]
NPT3085 Organism Penicillium oxalicum Penicillium oxalicum IZ = 20.0 mm PMID[573706]
NPT3085 Organism Penicillium oxalicum Penicillium oxalicum IZ = 6.0 mm PMID[573706]
NPT2 Others Unspecified Activity = 3.4 % PMID[573706]
NPT2 Others Unspecified IC50 = 600.0 nM PMID[573706]
NPT2 Others Unspecified IC50 = 1500.0 nM PMID[573706]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum Activity > 50.0 % PMID[573706]
NPT1513 Organism Mycobacterium avium Mycobacterium avium IC50 = 350000.0 nM PMID[573706]
NPT2 Others Unspecified IC50 = 76000.0 nM PMID[573706]

☑ 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 NPC225022 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 NPC238554
0.9714 High Similarity NPC177030
0.9315 High Similarity NPC24827
0.9315 High Similarity NPC228902
0.9155 High Similarity NPC162571
0.9155 High Similarity NPC112983
0.9067 High Similarity NPC199134
0.9067 High Similarity NPC286816
0.8873 High Similarity NPC494
0.8514 High Similarity NPC146583
0.8429 Intermediate Similarity NPC173409
0.8429 Intermediate Similarity NPC53136
0.8205 Intermediate Similarity NPC85743
0.8205 Intermediate Similarity NPC102065
0.8143 Intermediate Similarity NPC217537
0.8133 Intermediate Similarity NPC269103
0.8133 Intermediate Similarity NPC124072
0.7763 Intermediate Similarity NPC299932
0.7763 Intermediate Similarity NPC475113
0.7568 Intermediate Similarity NPC475110
0.7564 Intermediate Similarity NPC144419
0.7468 Intermediate Similarity NPC188354
0.7375 Intermediate Similarity NPC469414
0.7375 Intermediate Similarity NPC329826
0.7273 Intermediate Similarity NPC287705
0.7273 Intermediate Similarity NPC238223
0.7273 Intermediate Similarity NPC474823
0.7237 Intermediate Similarity NPC37382
0.7179 Intermediate Similarity NPC475004
0.7176 Intermediate Similarity NPC8161
0.716 Intermediate Similarity NPC478193
0.716 Intermediate Similarity NPC478191
0.716 Intermediate Similarity NPC478196
0.716 Intermediate Similarity NPC478194
0.716 Intermediate Similarity NPC478195
0.716 Intermediate Similarity NPC478192
0.716 Intermediate Similarity NPC161038
0.7143 Intermediate Similarity NPC132286
0.7067 Intermediate Similarity NPC473737
0.7033 Intermediate Similarity NPC303230
0.7033 Intermediate Similarity NPC114345
0.7033 Intermediate Similarity NPC6099
0.7 Intermediate Similarity NPC133098
0.6988 Remote Similarity NPC275530
0.6951 Remote Similarity NPC260396
0.6941 Remote Similarity NPC47653
0.6883 Remote Similarity NPC470123
0.6883 Remote Similarity NPC282760
0.6867 Remote Similarity NPC301207
0.6848 Remote Similarity NPC327760
0.6842 Remote Similarity NPC68110
0.679 Remote Similarity NPC293114
0.6786 Remote Similarity NPC68156
0.6786 Remote Similarity NPC125365
0.6786 Remote Similarity NPC176329
0.6786 Remote Similarity NPC474818
0.6786 Remote Similarity NPC49302
0.6786 Remote Similarity NPC51809
0.675 Remote Similarity NPC236208
0.675 Remote Similarity NPC473277
0.6747 Remote Similarity NPC329852
0.6742 Remote Similarity NPC470755
0.6739 Remote Similarity NPC475879
0.6706 Remote Similarity NPC279214
0.6706 Remote Similarity NPC221095
0.6706 Remote Similarity NPC473471
0.6667 Remote Similarity NPC318306
0.6667 Remote Similarity NPC205615
0.6667 Remote Similarity NPC150502
0.6667 Remote Similarity NPC256640
0.6667 Remote Similarity NPC127118
0.6667 Remote Similarity NPC476589
0.6667 Remote Similarity NPC131174
0.6667 Remote Similarity NPC209113
0.6667 Remote Similarity NPC16279
0.663 Remote Similarity NPC225283
0.6629 Remote Similarity NPC158756
0.6628 Remote Similarity NPC99651
0.6628 Remote Similarity NPC63326
0.6628 Remote Similarity NPC265980
0.6627 Remote Similarity NPC476590
0.6627 Remote Similarity NPC227396
0.6627 Remote Similarity NPC114727
0.6627 Remote Similarity NPC470686
0.6625 Remote Similarity NPC218477
0.6623 Remote Similarity NPC2328
0.6591 Remote Similarity NPC310450
0.6591 Remote Similarity NPC475046
0.6591 Remote Similarity NPC474959
0.6591 Remote Similarity NPC11383
0.6588 Remote Similarity NPC315394
0.6588 Remote Similarity NPC7563
0.6588 Remote Similarity NPC320630
0.6588 Remote Similarity NPC116177
0.6585 Remote Similarity NPC316185
0.6585 Remote Similarity NPC320119
0.6582 Remote Similarity NPC248125
0.6582 Remote Similarity NPC146811
0.6579 Remote Similarity NPC130953
0.6559 Remote Similarity NPC3436
0.6522 Remote Similarity NPC476805
0.6522 Remote Similarity NPC475819
0.6522 Remote Similarity NPC260343
0.6517 Remote Similarity NPC286770
0.6517 Remote Similarity NPC169575
0.6517 Remote Similarity NPC229799
0.6517 Remote Similarity NPC284472
0.6517 Remote Similarity NPC40746
0.6517 Remote Similarity NPC16488
0.6512 Remote Similarity NPC471465
0.6512 Remote Similarity NPC93763
0.6512 Remote Similarity NPC196653
0.6512 Remote Similarity NPC182292
0.6512 Remote Similarity NPC264391
0.6512 Remote Similarity NPC127526
0.6512 Remote Similarity NPC315765
0.6512 Remote Similarity NPC108816
0.6506 Remote Similarity NPC284006
0.6494 Remote Similarity NPC151648
0.6494 Remote Similarity NPC113293
0.6489 Remote Similarity NPC472814
0.6489 Remote Similarity NPC470520
0.6489 Remote Similarity NPC177037
0.6486 Remote Similarity NPC40148
0.6484 Remote Similarity NPC315395
0.6484 Remote Similarity NPC469483
0.6484 Remote Similarity NPC469910
0.6484 Remote Similarity NPC261721
0.6484 Remote Similarity NPC316426
0.6477 Remote Similarity NPC24417
0.6477 Remote Similarity NPC297440
0.6477 Remote Similarity NPC325031
0.6471 Remote Similarity NPC68819
0.6471 Remote Similarity NPC470705
0.6463 Remote Similarity NPC202011
0.6463 Remote Similarity NPC476037
0.6456 Remote Similarity NPC133904
0.6456 Remote Similarity NPC182794
0.6456 Remote Similarity NPC471556
0.6444 Remote Similarity NPC31086
0.6444 Remote Similarity NPC163093
0.6437 Remote Similarity NPC167881
0.6437 Remote Similarity NPC98557
0.6429 Remote Similarity NPC315843
0.6421 Remote Similarity NPC115021
0.6421 Remote Similarity NPC59646
0.642 Remote Similarity NPC63873
0.6413 Remote Similarity NPC45409
0.6404 Remote Similarity NPC473529
0.6404 Remote Similarity NPC473712
0.6404 Remote Similarity NPC473780
0.6404 Remote Similarity NPC229825
0.6404 Remote Similarity NPC180363
0.6404 Remote Similarity NPC94875
0.6404 Remote Similarity NPC475159
0.6404 Remote Similarity NPC131002
0.6404 Remote Similarity NPC329829
0.6404 Remote Similarity NPC73310
0.6404 Remote Similarity NPC11332
0.6404 Remote Similarity NPC145914
0.6404 Remote Similarity NPC65930
0.6386 Remote Similarity NPC84038
0.6386 Remote Similarity NPC186531
0.6383 Remote Similarity NPC274075
0.6375 Remote Similarity NPC315115
0.6375 Remote Similarity NPC276299
0.6374 Remote Similarity NPC120398
0.6374 Remote Similarity NPC477014
0.6374 Remote Similarity NPC261380
0.6374 Remote Similarity NPC471567
0.6374 Remote Similarity NPC477013
0.6374 Remote Similarity NPC307126
0.6374 Remote Similarity NPC68303
0.6364 Remote Similarity NPC98519
0.6364 Remote Similarity NPC469864
0.6364 Remote Similarity NPC121374
0.6364 Remote Similarity NPC327112
0.6364 Remote Similarity NPC469872
0.6354 Remote Similarity NPC469632
0.6354 Remote Similarity NPC475832
0.6354 Remote Similarity NPC475927
0.6354 Remote Similarity NPC470521
0.6353 Remote Similarity NPC473948
0.6344 Remote Similarity NPC476803
0.6344 Remote Similarity NPC475739
0.6341 Remote Similarity NPC143396
0.6341 Remote Similarity NPC475982
0.6333 Remote Similarity NPC116543
0.6333 Remote Similarity NPC253801
0.6333 Remote Similarity NPC131669
0.6333 Remote Similarity NPC144415
0.6333 Remote Similarity NPC473390
0.6333 Remote Similarity NPC59097
0.6327 Remote Similarity NPC53844
0.6322 Remote Similarity NPC267231
0.6316 Remote Similarity NPC2882
0.6316 Remote Similarity NPC32552
0.631 Remote Similarity NPC238948
0.631 Remote Similarity NPC329890
0.631 Remote Similarity NPC474705

  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 NPC225022 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
0.6364 Remote Similarity NPD4246 Clinical (unspecified phase)
0.6098 Remote Similarity NPD4247 Clinical (unspecified phase)
0.6044 Remote Similarity NPD5209 Approved
0.6023 Remote Similarity NPD4756 Discovery
0.5978 Remote Similarity NPD7154 Phase 3
0.5876 Remote Similarity NPD5785 Approved
0.5816 Remote Similarity NPD7983 Approved
0.58 Remote Similarity NPD1698 Clinical (unspecified phase)
0.5758 Remote Similarity NPD5778 Approved
0.5758 Remote Similarity NPD5779 Approved
0.5745 Remote Similarity NPD6400 Clinical (unspecified phase)
0.5714 Remote Similarity NPD6698 Approved
0.5714 Remote Similarity NPD46 Approved
0.5696 Remote Similarity NPD69 Approved
0.5696 Remote Similarity NPD9119 Approved
0.5684 Remote Similarity NPD5363 Approved
0.5663 Remote Similarity NPD2685 Clinical (unspecified phase)
0.5657 Remote Similarity NPD7637 Suspended
0.5652 Remote Similarity NPD4252 Approved
0.5652 Remote Similarity NPD5790 Clinical (unspecified phase)
0.5631 Remote Similarity NPD4225 Approved
0.5619 Remote Similarity NPD7632 Discontinued
0.56 Remote Similarity NPD6927 Phase 3

  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