Structure

Physi-Chem Properties

Molecular Weight:  371.89
Volume:  218.686
LogP:  3.082
LogD:  1.621
LogS:  -3.227
# 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:  0.612
Synthetic Accessibility Score:  4.081
Fsp3:  0.444
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.432
MDCK Permeability:  2.1741514501627535e-05
Pgp-inhibitor:  0.183
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.334
30% Bioavailability (F30%):  0.975

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.635
Plasma Protein Binding (PPB):  91.96329498291016%
Volume Distribution (VD):  0.525
Pgp-substrate:  16.720033645629883%

ADMET: Metabolism

CYP1A2-inhibitor:  0.96
CYP1A2-substrate:  0.659
CYP2C19-inhibitor:  0.769
CYP2C19-substrate:  0.25
CYP2C9-inhibitor:  0.612
CYP2C9-substrate:  0.227
CYP2D6-inhibitor:  0.301
CYP2D6-substrate:  0.124
CYP3A4-inhibitor:  0.189
CYP3A4-substrate:  0.185

ADMET: Excretion

Clearance (CL):  2.059
Half-life (T1/2):  0.382

ADMET: Toxicity

hERG Blockers:  0.001
Human Hepatotoxicity (H-HT):  0.875
Drug-inuced Liver Injury (DILI):  0.858
AMES Toxicity:  0.949
Rat Oral Acute Toxicity:  0.988
Maximum Recommended Daily Dose:  0.962
Skin Sensitization:  0.945
Carcinogencity:  0.858
Eye Corrosion:  0.946
Eye Irritation:  0.988
Respiratory Toxicity:  0.949

Download Data

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

  Natural Product: NPC24827

Natural Product ID:  NPC24827
Common Name*:   (R,Z)-4-Bromo-3-(1-Hydroxybutyl)-5-(Iodomethylene)Furan-2(5H)-One
IUPAC Name:   (5Z)-4-bromo-3-[(1R)-1-hydroxybutyl]-5-(iodomethylidene)furan-2-one
Synonyms:  
Standard InCHIKey:  KCFLZMAPXDKUEQ-WEWOIACBSA-N
Standard InCHI:  InChI=1S/C9H10BrIO3/c1-2-3-5(12)7-8(10)6(4-11)14-9(7)13/h4-5,12H,2-3H2,1H3/b6-4-/t5-/m1/s1
SMILES:  CCC[C@H](C1=C(/C(=C/I)/OC1=O)Br)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL505711
PubChem CID:   21729107
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 = 1.3 ug ml-1 PMID[496498]
NPT91 Cell Line KB Homo sapiens ED50 = 0.4 ug ml-1 PMID[496498]
NPT91 Cell Line KB Homo sapiens ED50 = 4.1 ug ml-1 PMID[496498]
NPT91 Cell Line KB Homo sapiens ED50 = 0.3 ug ml-1 PMID[496498]
NPT858 Cell Line LNCaP Homo sapiens ED50 < 0.1 ug ml-1 PMID[496498]
NPT133 Cell Line ZR-75-1 Homo sapiens ED50 = 0.3 ug ml-1 PMID[496498]
NPT459 Individual Protein Human immunodeficiency virus type 1 reverse transcriptase Human immunodeficiency virus 1 IC50 = 700000.0 nM PMID[496498]
NPT3085 Organism Penicillium oxalicum Penicillium oxalicum IZ = 20.0 mm PMID[496498]
NPT3085 Organism Penicillium oxalicum Penicillium oxalicum IZ = 18.0 mm PMID[496498]
NPT3085 Organism Penicillium oxalicum Penicillium oxalicum IZ = 12.0 mm PMID[496498]
NPT3085 Organism Penicillium oxalicum Penicillium oxalicum IZ = 4.0 mm PMID[496498]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 6.8 ug.mL-1 PMID[496498]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 > 10.0 ug.mL-1 PMID[496498]
NPT2 Others Unspecified Ratio IC50 < 1.0 n.a. PMID[496498]
NPT2 Others Unspecified Activity = 4.2 % PMID[496498]

☑ 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 NPC24827 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 NPC228902
0.9315 High Similarity NPC238554
0.9315 High Similarity NPC225022
0.9306 High Similarity NPC177030
0.9167 High Similarity NPC146583
0.8947 High Similarity NPC286816
0.8947 High Similarity NPC199134
0.8816 High Similarity NPC102065
0.8816 High Similarity NPC85743
0.8514 High Similarity NPC112983
0.8514 High Similarity NPC162571
0.8493 Intermediate Similarity NPC494
0.8052 Intermediate Similarity NPC188354
0.7808 Intermediate Similarity NPC53136
0.7808 Intermediate Similarity NPC173409
0.7778 Intermediate Similarity NPC217537
0.7662 Intermediate Similarity NPC299932
0.7662 Intermediate Similarity NPC475113
0.7564 Intermediate Similarity NPC124072
0.7564 Intermediate Similarity NPC269103
0.7468 Intermediate Similarity NPC144419
0.7284 Intermediate Similarity NPC469414
0.7284 Intermediate Similarity NPC329826
0.7179 Intermediate Similarity NPC238223
0.7179 Intermediate Similarity NPC474823
0.7179 Intermediate Similarity NPC287705
0.7143 Intermediate Similarity NPC37382
0.7089 Intermediate Similarity NPC475004
0.7073 Intermediate Similarity NPC161038
0.7073 Intermediate Similarity NPC478194
0.7073 Intermediate Similarity NPC478191
0.7073 Intermediate Similarity NPC478193
0.7073 Intermediate Similarity NPC478196
0.7073 Intermediate Similarity NPC478195
0.7073 Intermediate Similarity NPC478192
0.7051 Intermediate Similarity NPC132286
0.7013 Intermediate Similarity NPC475110
0.6974 Remote Similarity NPC473737
0.6957 Remote Similarity NPC303230
0.6957 Remote Similarity NPC6099
0.6957 Remote Similarity NPC114345
0.6914 Remote Similarity NPC133098
0.6905 Remote Similarity NPC275530
0.6897 Remote Similarity NPC8161
0.6867 Remote Similarity NPC260396
0.686 Remote Similarity NPC47653
0.6795 Remote Similarity NPC282760
0.6795 Remote Similarity NPC470123
0.6786 Remote Similarity NPC301207
0.6774 Remote Similarity NPC327760
0.6753 Remote Similarity NPC68110
0.6707 Remote Similarity NPC293114
0.6706 Remote Similarity NPC49302
0.6706 Remote Similarity NPC68156
0.6706 Remote Similarity NPC474818
0.6706 Remote Similarity NPC125365
0.6706 Remote Similarity NPC51809
0.6706 Remote Similarity NPC176329
0.6705 Remote Similarity NPC26624
0.6667 Remote Similarity NPC470755
0.6667 Remote Similarity NPC329852
0.6667 Remote Similarity NPC475879
0.6667 Remote Similarity NPC236208
0.6667 Remote Similarity NPC473277
0.6628 Remote Similarity NPC279214
0.6628 Remote Similarity NPC221095
0.6628 Remote Similarity NPC473471
0.6591 Remote Similarity NPC150502
0.6588 Remote Similarity NPC209113
0.6588 Remote Similarity NPC205615
0.6588 Remote Similarity NPC16279
0.6588 Remote Similarity NPC127118
0.6588 Remote Similarity NPC51391
0.6588 Remote Similarity NPC256640
0.6588 Remote Similarity NPC4492
0.6582 Remote Similarity NPC131174
0.6582 Remote Similarity NPC476589
0.6579 Remote Similarity NPC318306
0.6559 Remote Similarity NPC225283
0.6556 Remote Similarity NPC158756
0.6552 Remote Similarity NPC99651
0.6552 Remote Similarity NPC265980
0.6552 Remote Similarity NPC63326
0.6548 Remote Similarity NPC114727
0.6548 Remote Similarity NPC227396
0.6548 Remote Similarity NPC470686
0.6548 Remote Similarity NPC476590
0.6543 Remote Similarity NPC218477
0.6538 Remote Similarity NPC2328
0.6517 Remote Similarity NPC11383
0.6517 Remote Similarity NPC474959
0.6517 Remote Similarity NPC310450
0.6517 Remote Similarity NPC475046
0.6512 Remote Similarity NPC320630
0.6512 Remote Similarity NPC116177
0.6512 Remote Similarity NPC315394
0.6512 Remote Similarity NPC7563
0.6506 Remote Similarity NPC320119
0.6506 Remote Similarity NPC316185
0.65 Remote Similarity NPC146811
0.65 Remote Similarity NPC248125
0.6494 Remote Similarity NPC130953
0.6489 Remote Similarity NPC3436
0.6452 Remote Similarity NPC475819
0.6452 Remote Similarity NPC260343
0.6452 Remote Similarity NPC476805
0.6444 Remote Similarity NPC40746
0.6444 Remote Similarity NPC284472
0.6444 Remote Similarity NPC286770
0.6444 Remote Similarity NPC16488
0.6444 Remote Similarity NPC169575
0.6444 Remote Similarity NPC229799
0.6437 Remote Similarity NPC196653
0.6437 Remote Similarity NPC182292
0.6437 Remote Similarity NPC315765
0.6437 Remote Similarity NPC127526
0.6437 Remote Similarity NPC108816
0.6437 Remote Similarity NPC471465
0.6437 Remote Similarity NPC264391
0.6437 Remote Similarity NPC93763
0.6429 Remote Similarity NPC284006
0.6421 Remote Similarity NPC470520
0.6421 Remote Similarity NPC177037
0.6421 Remote Similarity NPC472814
0.6413 Remote Similarity NPC469483
0.6413 Remote Similarity NPC469910
0.6413 Remote Similarity NPC261721
0.6413 Remote Similarity NPC315395
0.6413 Remote Similarity NPC316426
0.641 Remote Similarity NPC113293
0.641 Remote Similarity NPC151648
0.6404 Remote Similarity NPC24417
0.6404 Remote Similarity NPC325031
0.6404 Remote Similarity NPC297440
0.64 Remote Similarity NPC40148
0.6395 Remote Similarity NPC470705
0.6395 Remote Similarity NPC68819
0.6386 Remote Similarity NPC202011
0.6386 Remote Similarity NPC476037
0.6375 Remote Similarity NPC471556
0.6375 Remote Similarity NPC133904
0.6375 Remote Similarity NPC182794
0.6374 Remote Similarity NPC31086
0.6374 Remote Similarity NPC163093
0.6364 Remote Similarity NPC98557
0.6364 Remote Similarity NPC167881
0.6354 Remote Similarity NPC115021
0.6354 Remote Similarity NPC59646
0.6353 Remote Similarity NPC315843
0.6344 Remote Similarity NPC45409
0.6341 Remote Similarity NPC63873
0.6333 Remote Similarity NPC473712
0.6333 Remote Similarity NPC65930
0.6333 Remote Similarity NPC131002
0.6333 Remote Similarity NPC475159
0.6333 Remote Similarity NPC94875
0.6333 Remote Similarity NPC11332
0.6333 Remote Similarity NPC145914
0.6333 Remote Similarity NPC473780
0.6333 Remote Similarity NPC180363
0.6333 Remote Similarity NPC229825
0.6333 Remote Similarity NPC73310
0.6333 Remote Similarity NPC473529
0.6333 Remote Similarity NPC329829
0.6316 Remote Similarity NPC274075
0.631 Remote Similarity NPC84038
0.631 Remote Similarity NPC186531
0.6304 Remote Similarity NPC120398
0.6304 Remote Similarity NPC307126
0.6304 Remote Similarity NPC261380
0.6304 Remote Similarity NPC471567
0.6304 Remote Similarity NPC68303
0.6304 Remote Similarity NPC477014
0.6304 Remote Similarity NPC477013
0.63 Remote Similarity NPC469872
0.63 Remote Similarity NPC469864
0.6296 Remote Similarity NPC315115
0.6296 Remote Similarity NPC276299
0.6292 Remote Similarity NPC121374
0.6289 Remote Similarity NPC469632
0.6289 Remote Similarity NPC475927
0.6289 Remote Similarity NPC470521
0.6289 Remote Similarity NPC475832
0.6282 Remote Similarity NPC327112
0.6282 Remote Similarity NPC98519
0.6279 Remote Similarity NPC473948
0.6277 Remote Similarity NPC475739
0.6277 Remote Similarity NPC476803
0.6265 Remote Similarity NPC475982
0.6265 Remote Similarity NPC143396
0.6264 Remote Similarity NPC131669
0.6264 Remote Similarity NPC144415
0.6264 Remote Similarity NPC59097
0.6264 Remote Similarity NPC473390
0.6264 Remote Similarity NPC253801
0.6264 Remote Similarity NPC116543
0.6263 Remote Similarity NPC53844
0.625 Remote Similarity NPC2882
0.625 Remote Similarity NPC267231
0.625 Remote Similarity NPC32552

  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 NPC24827 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
0.6282 Remote Similarity NPD4246 Clinical (unspecified phase)
0.6024 Remote Similarity NPD4247 Clinical (unspecified phase)
0.5978 Remote Similarity NPD5209 Approved
0.5955 Remote Similarity NPD4756 Discovery
0.5914 Remote Similarity NPD7154 Phase 3
0.5816 Remote Similarity NPD5785 Approved
0.5758 Remote Similarity NPD7983 Approved
0.5743 Remote Similarity NPD1698 Clinical (unspecified phase)
0.57 Remote Similarity NPD5779 Approved
0.57 Remote Similarity NPD5778 Approved
0.5684 Remote Similarity NPD6400 Clinical (unspecified phase)
0.5657 Remote Similarity NPD46 Approved
0.5657 Remote Similarity NPD6698 Approved
0.5625 Remote Similarity NPD9119 Approved
0.5625 Remote Similarity NPD69 Approved
0.5625 Remote Similarity NPD5363 Approved
0.56 Remote Similarity NPD7637 Suspended

  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