Structure

Physi-Chem Properties

Molecular Weight:  403.91
Volume:  247.408
LogP:  2.33
LogD:  1.29
LogS:  -3.114
# Rotatable Bonds:  5
TPSA:  55.76
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.433
Synthetic Accessibility Score:  4.477
Fsp3:  0.7
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:  -4.468
MDCK Permeability:  1.9844006601488218e-05
Pgp-inhibitor:  0.068
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.012
20% Bioavailability (F20%):  0.289
30% Bioavailability (F30%):  0.823

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.975
Plasma Protein Binding (PPB):  60.08030319213867%
Volume Distribution (VD):  1.226
Pgp-substrate:  52.79338836669922%

ADMET: Metabolism

CYP1A2-inhibitor:  0.526
CYP1A2-substrate:  0.808
CYP2C19-inhibitor:  0.568
CYP2C19-substrate:  0.847
CYP2C9-inhibitor:  0.321
CYP2C9-substrate:  0.073
CYP2D6-inhibitor:  0.019
CYP2D6-substrate:  0.175
CYP3A4-inhibitor:  0.122
CYP3A4-substrate:  0.517

ADMET: Excretion

Clearance (CL):  5.218
Half-life (T1/2):  0.778

ADMET: Toxicity

hERG Blockers:  0.013
Human Hepatotoxicity (H-HT):  0.343
Drug-inuced Liver Injury (DILI):  0.925
AMES Toxicity:  0.985
Rat Oral Acute Toxicity:  0.872
Maximum Recommended Daily Dose:  0.922
Skin Sensitization:  0.9
Carcinogencity:  0.756
Eye Corrosion:  0.936
Eye Irritation:  0.937
Respiratory Toxicity:  0.911

Download Data

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

  Natural Product: NPC85743

Natural Product ID:  NPC85743
Common Name*:   (5R)-4-Bromo-3-[(1R)-1-Hydroxybutyl]-5-(Iodomethyl)-5-Methoxyfuran-2-One
IUPAC Name:   (5R)-4-bromo-3-[(1R)-1-hydroxybutyl]-5-(iodomethyl)-5-methoxyfuran-2-one
Synonyms:  
Standard InCHIKey:  YRYRVZXFQIQXET-LDWIPMOCSA-N
Standard InCHI:  InChI=1S/C10H14BrIO4/c1-3-4-6(13)7-8(11)10(5-12,15-2)16-9(7)14/h6,13H,3-5H2,1-2H3/t6-,10+/m1/s1
SMILES:  CCC[C@H](C1=C(Br)[C@@](OC1=O)(CI)OC)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL526844
PubChem CID:   21773478
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
NPT3085 Organism Penicillium oxalicum Penicillium oxalicum IZ = 14.0 mm PMID[523203]
NPT3085 Organism Penicillium oxalicum Penicillium oxalicum IZ = 16.0 mm PMID[523203]
NPT3085 Organism Penicillium oxalicum Penicillium oxalicum IZ = 10.0 mm PMID[523203]
NPT2 Others Unspecified Activity = 77.2 % PMID[523203]

☑ 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 NPC85743 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 NPC102065
0.9178 High Similarity NPC188354
0.8816 High Similarity NPC24827
0.8816 High Similarity NPC228902
0.8767 High Similarity NPC299932
0.8767 High Similarity NPC475113
0.8649 High Similarity NPC269103
0.8649 High Similarity NPC124072
0.8421 Intermediate Similarity NPC177030
0.8289 Intermediate Similarity NPC146583
0.8205 Intermediate Similarity NPC238554
0.8205 Intermediate Similarity NPC225022
0.7901 Intermediate Similarity NPC286816
0.7901 Intermediate Similarity NPC199134
0.7895 Intermediate Similarity NPC494
0.7838 Intermediate Similarity NPC475110
0.7692 Intermediate Similarity NPC162571
0.7692 Intermediate Similarity NPC112983
0.7595 Intermediate Similarity NPC144419
0.7011 Intermediate Similarity NPC310450
0.7011 Intermediate Similarity NPC475046
0.7011 Intermediate Similarity NPC11383
0.7011 Intermediate Similarity NPC474959
0.6977 Remote Similarity NPC47653
0.6974 Remote Similarity NPC217537
0.6932 Remote Similarity NPC284472
0.6932 Remote Similarity NPC286770
0.6932 Remote Similarity NPC229799
0.6795 Remote Similarity NPC173409
0.6795 Remote Similarity NPC53136
0.6709 Remote Similarity NPC282760
0.6709 Remote Similarity NPC470123
0.6667 Remote Similarity NPC473334
0.6667 Remote Similarity NPC68110
0.6629 Remote Similarity NPC26624
0.6628 Remote Similarity NPC10572
0.6598 Remote Similarity NPC17578
0.6598 Remote Similarity NPC240673
0.6596 Remote Similarity NPC475879
0.6593 Remote Similarity NPC470755
0.6588 Remote Similarity NPC161038
0.6562 Remote Similarity NPC475927
0.6562 Remote Similarity NPC475832
0.6562 Remote Similarity NPC474555
0.6512 Remote Similarity NPC205615
0.6512 Remote Similarity NPC256640
0.6512 Remote Similarity NPC16279
0.6484 Remote Similarity NPC158756
0.6477 Remote Similarity NPC99651
0.6471 Remote Similarity NPC476590
0.6471 Remote Similarity NPC114727
0.6463 Remote Similarity NPC238223
0.6463 Remote Similarity NPC474823
0.6444 Remote Similarity NPC8161
0.6444 Remote Similarity NPC471296
0.6437 Remote Similarity NPC275530
0.642 Remote Similarity NPC248125
0.642 Remote Similarity NPC37382
0.6395 Remote Similarity NPC469414
0.6395 Remote Similarity NPC478193
0.6395 Remote Similarity NPC478191
0.6395 Remote Similarity NPC478192
0.6395 Remote Similarity NPC478195
0.6395 Remote Similarity NPC478196
0.6395 Remote Similarity NPC478194
0.6395 Remote Similarity NPC329852
0.6395 Remote Similarity NPC329826
0.6395 Remote Similarity NPC260396
0.6392 Remote Similarity NPC474554
0.6392 Remote Similarity NPC471496
0.6386 Remote Similarity NPC475004
0.6383 Remote Similarity NPC475819
0.6383 Remote Similarity NPC476805
0.6374 Remote Similarity NPC40746
0.6374 Remote Similarity NPC169575
0.6364 Remote Similarity NPC93763
0.6364 Remote Similarity NPC127526
0.6364 Remote Similarity NPC108816
0.6364 Remote Similarity NPC475709
0.6354 Remote Similarity NPC470520
0.6354 Remote Similarity NPC141831
0.6354 Remote Similarity NPC114345
0.6354 Remote Similarity NPC303230
0.6354 Remote Similarity NPC6099
0.6344 Remote Similarity NPC469483
0.6344 Remote Similarity NPC469910
0.6344 Remote Similarity NPC261721
0.6341 Remote Similarity NPC132286
0.6333 Remote Similarity NPC297440
0.6333 Remote Similarity NPC150502
0.6333 Remote Similarity NPC24417
0.6327 Remote Similarity NPC476487
0.6327 Remote Similarity NPC476488
0.6322 Remote Similarity NPC68819
0.6322 Remote Similarity NPC301207
0.6316 Remote Similarity NPC139418
0.6316 Remote Similarity NPC225283
0.6316 Remote Similarity NPC40148
0.631 Remote Similarity NPC202011
0.6304 Remote Similarity NPC31086
0.6304 Remote Similarity NPC163093
0.6292 Remote Similarity NPC63326
0.6292 Remote Similarity NPC265980
0.6277 Remote Similarity NPC475037
0.6277 Remote Similarity NPC45409
0.6275 Remote Similarity NPC313569
0.6265 Remote Similarity NPC218477
0.6265 Remote Similarity NPC287705
0.6264 Remote Similarity NPC94875
0.6264 Remote Similarity NPC145914
0.6264 Remote Similarity NPC475159
0.6264 Remote Similarity NPC473780
0.6264 Remote Similarity NPC473712
0.6264 Remote Similarity NPC329829
0.6264 Remote Similarity NPC131002
0.6264 Remote Similarity NPC65930
0.6264 Remote Similarity NPC229825
0.6264 Remote Similarity NPC180363
0.6264 Remote Similarity NPC473529
0.6264 Remote Similarity NPC11332
0.6264 Remote Similarity NPC73310
0.625 Remote Similarity NPC3436
0.625 Remote Similarity NPC116177
0.625 Remote Similarity NPC473737
0.625 Remote Similarity NPC7563
0.625 Remote Similarity NPC176329
0.625 Remote Similarity NPC473904
0.625 Remote Similarity NPC51809
0.625 Remote Similarity NPC320630
0.625 Remote Similarity NPC232426
0.625 Remote Similarity NPC281942
0.625 Remote Similarity NPC125365
0.625 Remote Similarity NPC474818
0.625 Remote Similarity NPC49302
0.6238 Remote Similarity NPC469864
0.6238 Remote Similarity NPC469872
0.6237 Remote Similarity NPC471300
0.6237 Remote Similarity NPC470124
0.6237 Remote Similarity NPC307126
0.6237 Remote Similarity NPC261380
0.6237 Remote Similarity NPC471567
0.6237 Remote Similarity NPC475034
0.6237 Remote Similarity NPC120398
0.6237 Remote Similarity NPC474860
0.6237 Remote Similarity NPC68303
0.6237 Remote Similarity NPC477014
0.6237 Remote Similarity NPC477013
0.6235 Remote Similarity NPC133098
0.6235 Remote Similarity NPC84038
0.6235 Remote Similarity NPC293114
0.6224 Remote Similarity NPC469632
0.6224 Remote Similarity NPC470521
0.6224 Remote Similarity NPC96541
0.6222 Remote Similarity NPC121374
0.622 Remote Similarity NPC276299
0.6211 Remote Similarity NPC476803
0.6207 Remote Similarity NPC473948
0.62 Remote Similarity NPC471462
0.6196 Remote Similarity NPC473390
0.6196 Remote Similarity NPC116543
0.6196 Remote Similarity NPC144415
0.6196 Remote Similarity NPC59097
0.6196 Remote Similarity NPC131669
0.6196 Remote Similarity NPC253801
0.619 Remote Similarity NPC473277
0.619 Remote Similarity NPC236208
0.619 Remote Similarity NPC475982
0.6186 Remote Similarity NPC177037
0.6186 Remote Similarity NPC473707
0.6186 Remote Similarity NPC472814
0.6186 Remote Similarity NPC327760
0.6184 Remote Similarity NPC49028
0.618 Remote Similarity NPC471465
0.618 Remote Similarity NPC279214
0.618 Remote Similarity NPC221095
0.618 Remote Similarity NPC473471
0.618 Remote Similarity NPC196653
0.6176 Remote Similarity NPC471075
0.617 Remote Similarity NPC305475
0.617 Remote Similarity NPC475461
0.617 Remote Similarity NPC477015
0.6163 Remote Similarity NPC474705
0.6162 Remote Similarity NPC469873
0.6154 Remote Similarity NPC52861
0.6154 Remote Similarity NPC325031
0.6146 Remote Similarity NPC14901
0.6146 Remote Similarity NPC212664
0.6146 Remote Similarity NPC87306
0.6146 Remote Similarity NPC130359
0.6145 Remote Similarity NPC203335
0.6136 Remote Similarity NPC127118
0.6136 Remote Similarity NPC51391
0.6136 Remote Similarity NPC271986
0.6136 Remote Similarity NPC209113
0.6136 Remote Similarity NPC4492
0.6136 Remote Similarity NPC49392
0.6136 Remote Similarity NPC190400
0.6129 Remote Similarity NPC141193
0.6129 Remote Similarity NPC191476
0.6129 Remote Similarity NPC475035

  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 NPC85743 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
0.5957 Remote Similarity NPD6400 Clinical (unspecified phase)
0.581 Remote Similarity NPD7632 Discontinued
0.5758 Remote Similarity NPD5785 Approved
0.575 Remote Similarity NPD69 Approved
0.575 Remote Similarity NPD9119 Approved
0.5686 Remote Similarity NPD1698 Clinical (unspecified phase)
0.5684 Remote Similarity NPD7154 Phase 3
0.5625 Remote Similarity NPD9118 Approved
0.561 Remote Similarity NPD4246 Clinical (unspecified phase)
0.56 Remote Similarity NPD46 Approved
0.56 Remote Similarity NPD6698 Approved

  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