Structure

Physi-Chem Properties

Molecular Weight:  440.82
Volume:  266.372
LogP:  3.363
LogD:  1.815
LogS:  -2.826
# Rotatable Bonds:  2
TPSA:  60.77
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  2
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.543
Synthetic Accessibility Score:  2.933
Fsp3:  0.364
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.902
MDCK Permeability:  1.7337139070150442e-05
Pgp-inhibitor:  0.006
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.559
20% Bioavailability (F20%):  0.019
30% Bioavailability (F30%):  0.01

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.482
Plasma Protein Binding (PPB):  98.60792541503906%
Volume Distribution (VD):  0.518
Pgp-substrate:  3.064541816711426%

ADMET: Metabolism

CYP1A2-inhibitor:  0.712
CYP1A2-substrate:  0.418
CYP2C19-inhibitor:  0.201
CYP2C19-substrate:  0.074
CYP2C9-inhibitor:  0.606
CYP2C9-substrate:  0.581
CYP2D6-inhibitor:  0.316
CYP2D6-substrate:  0.244
CYP3A4-inhibitor:  0.285
CYP3A4-substrate:  0.134

ADMET: Excretion

Clearance (CL):  1.203
Half-life (T1/2):  0.821

ADMET: Toxicity

hERG Blockers:  0.015
Human Hepatotoxicity (H-HT):  0.172
Drug-inuced Liver Injury (DILI):  0.054
AMES Toxicity:  0.016
Rat Oral Acute Toxicity:  0.052
Maximum Recommended Daily Dose:  0.022
Skin Sensitization:  0.916
Carcinogencity:  0.07
Eye Corrosion:  0.005
Eye Irritation:  0.029
Respiratory Toxicity:  0.067

Download Data

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

  Natural Product: NPC226514

Natural Product ID:  NPC226514
Common Name*:   1-(2,3,6-Tribromo-4,5-Dihydroxybenzyl)Pyrrolidin-2-One
IUPAC Name:   1-[(2,3,6-tribromo-4,5-dihydroxyphenyl)methyl]pyrrolidin-2-one
Synonyms:  
Standard InCHIKey:  VZZUKOXTBHFIKN-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C11H10Br3NO3/c12-7-5(4-15-3-1-2-6(15)16)8(13)10(17)11(18)9(7)14/h17-18H,1-4H2
SMILES:  O=C1CCCN1Cc1c(Br)c(O)c(c(c1Br)Br)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL228908
PubChem CID:   16757395
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0000134] Phenols
        • [CHEMONTID:0001286] Benzenediols
          • [CHEMONTID:0000135] Catechols

*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
NPO6092 Symphyocladia latiuscula Species Rhodomelaceae Eukaryota n.a. n.a. n.a. PMID[11141124]
NPO6092 Symphyocladia latiuscula Species Rhodomelaceae Eukaryota n.a. n.a. n.a. PMID[15844965]
NPO6092 Symphyocladia latiuscula Species Rhodomelaceae Eukaryota n.a. n.a. n.a. PMID[17602526]
NPO6092 Symphyocladia latiuscula Species Rhodomelaceae 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
NPT35 Others n.a. IC50 = 18500.0 nM PMID[505272]

☑ 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 NPC226514 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
0.85 High Similarity NPC475688
0.8293 Intermediate Similarity NPC475120
0.7771 Intermediate Similarity NPC473941
0.7725 Intermediate Similarity NPC288747
0.7605 Intermediate Similarity NPC191557
0.7518 Intermediate Similarity NPC50782
0.7467 Intermediate Similarity NPC105702
0.7297 Intermediate Similarity NPC84606
0.7288 Intermediate Similarity NPC249113
0.723 Intermediate Similarity NPC219444
0.7211 Intermediate Similarity NPC227976
0.7175 Intermediate Similarity NPC129885
0.7081 Intermediate Similarity NPC125852
0.7039 Intermediate Similarity NPC134219
0.7032 Intermediate Similarity NPC110800
0.6993 Remote Similarity NPC13004
0.6974 Remote Similarity NPC142776
0.6948 Remote Similarity NPC55113
0.6879 Remote Similarity NPC303011
0.681 Remote Similarity NPC79076
0.6797 Remote Similarity NPC137117
0.6753 Remote Similarity NPC220311
0.6667 Remote Similarity NPC271942
0.6667 Remote Similarity NPC47790
0.6667 Remote Similarity NPC168680
0.6624 Remote Similarity NPC150929
0.6582 Remote Similarity NPC474536
0.6582 Remote Similarity NPC85049
0.6582 Remote Similarity NPC474087
0.6579 Remote Similarity NPC474146
0.6543 Remote Similarity NPC199089
0.6541 Remote Similarity NPC226493
0.6541 Remote Similarity NPC160081
0.6513 Remote Similarity NPC117759
0.6497 Remote Similarity NPC43706
0.646 Remote Similarity NPC474135
0.6456 Remote Similarity NPC473708
0.6456 Remote Similarity NPC474147
0.6433 Remote Similarity NPC318965
0.642 Remote Similarity NPC163560
0.642 Remote Similarity NPC471328
0.642 Remote Similarity NPC244890
0.6405 Remote Similarity NPC38483
0.64 Remote Similarity NPC115803
0.638 Remote Similarity NPC245386
0.6364 Remote Similarity NPC470250
0.6341 Remote Similarity NPC470249
0.6341 Remote Similarity NPC470248
0.6303 Remote Similarity NPC224663
0.6277 Remote Similarity NPC80337
0.6258 Remote Similarity NPC243404
0.6228 Remote Similarity NPC160932
0.6211 Remote Similarity NPC230539
0.6209 Remote Similarity NPC79844
0.6196 Remote Similarity NPC300020
0.6196 Remote Similarity NPC302171
0.6196 Remote Similarity NPC33338
0.6185 Remote Similarity NPC473608
0.6178 Remote Similarity NPC136543
0.6173 Remote Similarity NPC474614
0.617 Remote Similarity NPC475466
0.6154 Remote Similarity NPC89341
0.6154 Remote Similarity NPC118794
0.6146 Remote Similarity NPC102245
0.6146 Remote Similarity NPC64066
0.6145 Remote Similarity NPC301050
0.6145 Remote Similarity NPC131204
0.6145 Remote Similarity NPC135006
0.6139 Remote Similarity NPC229213
0.6129 Remote Similarity NPC85276
0.6118 Remote Similarity NPC59387
0.6111 Remote Similarity NPC214553
0.6101 Remote Similarity NPC473572
0.6101 Remote Similarity NPC474169
0.6084 Remote Similarity NPC235633
0.6074 Remote Similarity NPC135173
0.6073 Remote Similarity NPC246591
0.6071 Remote Similarity NPC128877
0.6057 Remote Similarity NPC469711
0.6047 Remote Similarity NPC109346
0.6034 Remote Similarity NPC474535
0.6012 Remote Similarity NPC71629
0.6012 Remote Similarity NPC296085
0.6 Remote Similarity NPC475697
0.599 Remote Similarity NPC147847
0.5988 Remote Similarity NPC312155
0.5976 Remote Similarity NPC211468
0.5976 Remote Similarity NPC170170
0.5976 Remote Similarity NPC231572
0.5976 Remote Similarity NPC219233
0.5974 Remote Similarity NPC142599
0.5969 Remote Similarity NPC259071
0.5969 Remote Similarity NPC77435
0.5965 Remote Similarity NPC308571
0.5963 Remote Similarity NPC171372
0.5948 Remote Similarity NPC146422
0.5941 Remote Similarity NPC323123
0.5941 Remote Similarity NPC251439
0.5939 Remote Similarity NPC473724
0.5939 Remote Similarity NPC475735
0.5938 Remote Similarity NPC174607
0.5918 Remote Similarity NPC80514
0.5893 Remote Similarity NPC109580
0.5882 Remote Similarity NPC156356
0.5879 Remote Similarity NPC99280
0.5876 Remote Similarity NPC152947
0.5872 Remote Similarity NPC470247
0.5868 Remote Similarity NPC300678
0.5866 Remote Similarity NPC470708
0.5866 Remote Similarity NPC135103
0.5858 Remote Similarity NPC313694
0.5858 Remote Similarity NPC242159
0.5855 Remote Similarity NPC54543
0.5855 Remote Similarity NPC96275
0.5851 Remote Similarity NPC226001
0.5849 Remote Similarity NPC180207
0.5848 Remote Similarity NPC470709
0.5842 Remote Similarity NPC21885
0.5838 Remote Similarity NPC184632
0.5828 Remote Similarity NPC110131
0.5824 Remote Similarity NPC238412
0.582 Remote Similarity NPC298981
0.582 Remote Similarity NPC126128
0.582 Remote Similarity NPC207819
0.582 Remote Similarity NPC110454
0.582 Remote Similarity NPC473462
0.5817 Remote Similarity NPC473358
0.5808 Remote Similarity NPC318862
0.5808 Remote Similarity NPC43613
0.5805 Remote Similarity NPC294249
0.5801 Remote Similarity NPC147091
0.5798 Remote Similarity NPC476331
0.5795 Remote Similarity NPC321505
0.5795 Remote Similarity NPC179825
0.5795 Remote Similarity NPC191376
0.5793 Remote Similarity NPC236347
0.5793 Remote Similarity NPC323775
0.5787 Remote Similarity NPC227953
0.5783 Remote Similarity NPC474091
0.5783 Remote Similarity NPC120251
0.578 Remote Similarity NPC250597
0.5767 Remote Similarity NPC469979
0.5763 Remote Similarity NPC246587
0.5763 Remote Similarity NPC476571
0.5763 Remote Similarity NPC428
0.5763 Remote Similarity NPC24233
0.5763 Remote Similarity NPC135538
0.5763 Remote Similarity NPC147390
0.5759 Remote Similarity NPC283468
0.5758 Remote Similarity NPC16031
0.5758 Remote Similarity NPC161593
0.5758 Remote Similarity NPC172403
0.5758 Remote Similarity NPC202866
0.5758 Remote Similarity NPC145888
0.5754 Remote Similarity NPC119669
0.5749 Remote Similarity NPC308885
0.5749 Remote Similarity NPC255550
0.5731 Remote Similarity NPC28641
0.5731 Remote Similarity NPC194359
0.573 Remote Similarity NPC103379
0.573 Remote Similarity NPC477565
0.5729 Remote Similarity NPC214188
0.5729 Remote Similarity NPC74618
0.5729 Remote Similarity NPC301941
0.5723 Remote Similarity NPC122009
0.5722 Remote Similarity NPC121571
0.5722 Remote Similarity NPC133011
0.5722 Remote Similarity NPC82285
0.5722 Remote Similarity NPC8093
0.5714 Remote Similarity NPC186063
0.5714 Remote Similarity NPC217574
0.5714 Remote Similarity NPC208757
0.5714 Remote Similarity NPC225130
0.5714 Remote Similarity NPC130595
0.5714 Remote Similarity NPC93882
0.5714 Remote Similarity NPC37205
0.5714 Remote Similarity NPC160931
0.5707 Remote Similarity NPC249274
0.5707 Remote Similarity NPC205167
0.5706 Remote Similarity NPC180647
0.5706 Remote Similarity NPC470471
0.5705 Remote Similarity NPC471488
0.5701 Remote Similarity NPC223223
0.5698 Remote Similarity NPC220858
0.5698 Remote Similarity NPC192768
0.5698 Remote Similarity NPC88249
0.5698 Remote Similarity NPC151895
0.5698 Remote Similarity NPC97221
0.5689 Remote Similarity NPC160193
0.5687 Remote Similarity NPC100395
0.5687 Remote Similarity NPC268572
0.5686 Remote Similarity NPC471495
0.5682 Remote Similarity NPC146370
0.5682 Remote Similarity NPC185838
0.568 Remote Similarity NPC285078
0.568 Remote Similarity NPC313737
0.568 Remote Similarity NPC6854
0.5673 Remote Similarity NPC416184
0.5673 Remote Similarity NPC7018
0.5665 Remote Similarity NPC156055

  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 NPC226514 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
0.6648 Remote Similarity NPD4010 Discontinued
0.6395 Remote Similarity NPD824 Approved
0.6273 Remote Similarity NPD9718 Approved
0.6054 Remote Similarity NPD9244 Approved
0.5978 Remote Similarity NPD6688 Approved
0.5978 Remote Similarity NPD6687 Approved
0.5976 Remote Similarity NPD1632 Clinical (unspecified phase)
0.5963 Remote Similarity NPD5311 Approved
0.5963 Remote Similarity NPD5310 Approved
0.5948 Remote Similarity NPD9377 Approved
0.5948 Remote Similarity NPD9379 Approved
0.5926 Remote Similarity NPD3053 Approved
0.5926 Remote Similarity NPD3055 Approved
0.5924 Remote Similarity NPD1161 Approved
0.5864 Remote Similarity NPD9634 Clinical (unspecified phase)
0.5858 Remote Similarity NPD743 Approved
0.5839 Remote Similarity NPD2337 Clinical (unspecified phase)
0.5824 Remote Similarity NPD1169 Approved
0.5819 Remote Similarity NPD1670 Discontinued
0.5818 Remote Similarity NPD4207 Discontinued
0.5806 Remote Similarity NPD5137 Approved
0.5793 Remote Similarity NPD9619 Approved
0.5793 Remote Similarity NPD9621 Approved
0.5793 Remote Similarity NPD9620 Approved
0.5771 Remote Similarity NPD3845 Phase 1
0.5771 Remote Similarity NPD3141 Discontinued
0.5758 Remote Similarity NPD9569 Approved
0.5753 Remote Similarity NPD4166 Phase 2
0.5749 Remote Similarity NPD3144 Approved
0.5749 Remote Similarity NPD597 Approved
0.5749 Remote Similarity NPD598 Approved
0.5749 Remote Similarity NPD2028 Clinical (unspecified phase)
0.5749 Remote Similarity NPD601 Approved
0.5749 Remote Similarity NPD3145 Approved
0.5739 Remote Similarity NPD2421 Approved
0.5739 Remote Similarity NPD2420 Approved
0.5722 Remote Similarity NPD1337 Clinical (unspecified phase)
0.5714 Remote Similarity NPD1130 Approved
0.5714 Remote Similarity NPD1136 Approved
0.5714 Remote Similarity NPD2674 Phase 3
0.5714 Remote Similarity NPD1132 Approved
0.5699 Remote Similarity NPD7280 Phase 3
0.5699 Remote Similarity NPD7281 Phase 3
0.5689 Remote Similarity NPD9536 Phase 1
0.5689 Remote Similarity NPD9537 Phase 1
0.5682 Remote Similarity NPD2422 Clinical (unspecified phase)
0.5682 Remote Similarity NPD6884 Clinical (unspecified phase)
0.568 Remote Similarity NPD3062 Approved
0.568 Remote Similarity NPD3061 Approved
0.568 Remote Similarity NPD3059 Approved
0.5676 Remote Similarity NPD1168 Approved
0.5668 Remote Similarity NPD1293 Approved
0.5652 Remote Similarity NPD9384 Approved
0.5652 Remote Similarity NPD9381 Approved
0.5644 Remote Similarity NPD8095 Phase 1
0.5621 Remote Similarity NPD259 Phase 1
0.5614 Remote Similarity NPD823 Approved
0.5614 Remote Similarity NPD817 Approved
0.5614 Remote Similarity NPD5314 Approved
0.5614 Remote Similarity NPD2492 Phase 1
0.5602 Remote Similarity NPD257 Approved
0.5602 Remote Similarity NPD258 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