Structure

Physi-Chem Properties

Molecular Weight:  591.62
Volume:  305.965
LogP:  5.954
LogD:  2.844
LogS:  -6.22
# Rotatable Bonds:  2
TPSA:  49.69
# H-Bond Aceptor:  3
# H-Bond Donor:  2
# Rings:  2
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.38
Synthetic Accessibility Score:  2.974
Fsp3:  0.0
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.829
MDCK Permeability:  1.4983076653152239e-05
Pgp-inhibitor:  0.999
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.973
20% Bioavailability (F20%):  0.007
30% Bioavailability (F30%):  0.028

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.278
Plasma Protein Binding (PPB):  102.52243041992188%
Volume Distribution (VD):  3.472
Pgp-substrate:  6.982175827026367%

ADMET: Metabolism

CYP1A2-inhibitor:  0.961
CYP1A2-substrate:  0.141
CYP2C19-inhibitor:  0.727
CYP2C19-substrate:  0.091
CYP2C9-inhibitor:  0.868
CYP2C9-substrate:  0.801
CYP2D6-inhibitor:  0.069
CYP2D6-substrate:  0.569
CYP3A4-inhibitor:  0.11
CYP3A4-substrate:  0.152

ADMET: Excretion

Clearance (CL):  0.605
Half-life (T1/2):  0.275

ADMET: Toxicity

hERG Blockers:  0.031
Human Hepatotoxicity (H-HT):  0.224
Drug-inuced Liver Injury (DILI):  0.707
AMES Toxicity:  0.01
Rat Oral Acute Toxicity:  0.977
Maximum Recommended Daily Dose:  0.929
Skin Sensitization:  0.933
Carcinogencity:  0.105
Eye Corrosion:  0.095
Eye Irritation:  0.961
Respiratory Toxicity:  0.918

Download Data

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

  Natural Product: NPC474375

Natural Product ID:  NPC474375
Common Name*:   3,4,5-Tribromo-2-(3,6-Dibromo-2-Hydroxyphenoxy)Phenol
IUPAC Name:   3,4,5-tribromo-2-(3,6-dibromo-2-hydroxyphenoxy)phenol
Synonyms:  
Standard InCHIKey:  DBYWUMCJCNTOPW-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C12H5Br5O3/c13-4-1-2-5(14)11(10(4)19)20-12-7(18)3-6(15)8(16)9(12)17/h1-3,18-19H
SMILES:  C1=CC(=C(C(=C1Br)O)OC2=C(C(=C(C=C2O)Br)Br)Br)Br
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL465755
PubChem CID:   44566718
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0002279] Benzene and substituted derivatives
        • [CHEMONTID:0004155] Diphenylethers
          • [CHEMONTID:0001845] Bromodiphenyl ethers

*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
NPO8481 Phyllospongia dendyi Species Thorectidae Eukaryota n.a. Palau n.a. PMID[15043436]
NPO8481 Phyllospongia dendyi Species Thorectidae 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
NPT2 Others Unspecified IC50 = 20900.0 nM PMID[450634]
NPT2 Others Unspecified IC50 = 4200.0 nM PMID[450634]

☑ 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 NPC474375 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
0.9913 High Similarity NPC175520
0.9913 High Similarity NPC295879
0.9913 High Similarity NPC25134
0.9913 High Similarity NPC97157
0.9913 High Similarity NPC159866
0.9913 High Similarity NPC64130
0.9826 High Similarity NPC137922
0.9826 High Similarity NPC40302
0.9739 High Similarity NPC196371
0.9739 High Similarity NPC299939
0.9739 High Similarity NPC153580
0.9739 High Similarity NPC47769
0.9739 High Similarity NPC226737
0.9658 High Similarity NPC68350
0.9658 High Similarity NPC230013
0.9658 High Similarity NPC131940
0.9658 High Similarity NPC81149
0.9658 High Similarity NPC197576
0.9652 High Similarity NPC63317
0.9652 High Similarity NPC41232
0.9565 High Similarity NPC44270
0.9565 High Similarity NPC86007
0.9487 High Similarity NPC88733
0.9487 High Similarity NPC173511
0.9478 High Similarity NPC191194
0.9478 High Similarity NPC104124
0.9237 High Similarity NPC170824
0.8983 High Similarity NPC71186
0.896 High Similarity NPC178301
0.888 High Similarity NPC206183
0.888 High Similarity NPC222684
0.8814 High Similarity NPC264379
0.8729 High Similarity NPC162294
0.8644 High Similarity NPC221301
0.864 High Similarity NPC45728
0.8189 Intermediate Similarity NPC1744
0.8189 Intermediate Similarity NPC163019
0.8174 Intermediate Similarity NPC319933
0.8029 Intermediate Similarity NPC8577
0.7953 Intermediate Similarity NPC235166
0.7719 Intermediate Similarity NPC475466
0.7554 Intermediate Similarity NPC271942
0.7458 Intermediate Similarity NPC314803
0.7333 Intermediate Similarity NPC13004
0.7273 Intermediate Similarity NPC286337
0.7239 Intermediate Similarity NPC236265
0.723 Intermediate Similarity NPC152947
0.7214 Intermediate Similarity NPC245386
0.7194 Intermediate Similarity NPC303011
0.7119 Intermediate Similarity NPC114325
0.709 Intermediate Similarity NPC219444
0.7059 Intermediate Similarity NPC220311
0.7037 Intermediate Similarity NPC84606
0.6957 Remote Similarity NPC252149
0.6929 Remote Similarity NPC226493
0.6929 Remote Similarity NPC160081
0.6894 Remote Similarity NPC86947
0.6884 Remote Similarity NPC134219
0.687 Remote Similarity NPC50782
0.6857 Remote Similarity NPC85049
0.6828 Remote Similarity NPC168680
0.6803 Remote Similarity NPC89341
0.6791 Remote Similarity NPC38483
0.6783 Remote Similarity NPC319826
0.6781 Remote Similarity NPC160932
0.6767 Remote Similarity NPC151617
0.6767 Remote Similarity NPC76915
0.6746 Remote Similarity NPC307875
0.6731 Remote Similarity NPC474535
0.6723 Remote Similarity NPC318429
0.6714 Remote Similarity NPC473708
0.6714 Remote Similarity NPC474147
0.6711 Remote Similarity NPC473608
0.6691 Remote Similarity NPC205213
0.6691 Remote Similarity NPC142776
0.669 Remote Similarity NPC11449
0.6688 Remote Similarity NPC475697
0.6667 Remote Similarity NPC473572
0.6667 Remote Similarity NPC94217
0.6667 Remote Similarity NPC474169
0.6667 Remote Similarity NPC109346
0.6667 Remote Similarity NPC214289
0.6645 Remote Similarity NPC135103
0.6644 Remote Similarity NPC213471
0.6643 Remote Similarity NPC43706
0.6642 Remote Similarity NPC290451
0.6642 Remote Similarity NPC9248
0.6642 Remote Similarity NPC127389
0.6638 Remote Similarity NPC125306
0.6619 Remote Similarity NPC137117
0.6615 Remote Similarity NPC473358
0.661 Remote Similarity NPC206876
0.6594 Remote Similarity NPC47790
0.6594 Remote Similarity NPC229213
0.6591 Remote Similarity NPC33244
0.6591 Remote Similarity NPC471488
0.6585 Remote Similarity NPC469979
0.6569 Remote Similarity NPC205850
0.6569 Remote Similarity NPC227976
0.6552 Remote Similarity NPC244890
0.6552 Remote Similarity NPC163560
0.6545 Remote Similarity NPC298981
0.6545 Remote Similarity NPC473462
0.6545 Remote Similarity NPC126128
0.6545 Remote Similarity NPC207819
0.6545 Remote Similarity NPC110454
0.6538 Remote Similarity NPC54543
0.6538 Remote Similarity NPC246358
0.6538 Remote Similarity NPC233731
0.6538 Remote Similarity NPC7097
0.6538 Remote Similarity NPC36108
0.6522 Remote Similarity NPC145780
0.6519 Remote Similarity NPC293619
0.6512 Remote Similarity NPC124712
0.6503 Remote Similarity NPC105702
0.65 Remote Similarity NPC228972
0.65 Remote Similarity NPC122792
0.65 Remote Similarity NPC74478
0.65 Remote Similarity NPC213414
0.6486 Remote Similarity NPC156356
0.6485 Remote Similarity NPC226001
0.6479 Remote Similarity NPC78061
0.6479 Remote Similarity NPC159987
0.6479 Remote Similarity NPC122359
0.6475 Remote Similarity NPC105147
0.6475 Remote Similarity NPC228875
0.6475 Remote Similarity NPC126216
0.6471 Remote Similarity NPC470626
0.6467 Remote Similarity NPC250597
0.6462 Remote Similarity NPC471495
0.6454 Remote Similarity NPC194519
0.6454 Remote Similarity NPC3221
0.6454 Remote Similarity NPC87113
0.6449 Remote Similarity NPC307253
0.6439 Remote Similarity NPC139617
0.6439 Remote Similarity NPC156840
0.6439 Remote Similarity NPC78918
0.6439 Remote Similarity NPC257124
0.6439 Remote Similarity NPC195873
0.6439 Remote Similarity NPC173746
0.6439 Remote Similarity NPC8547
0.6438 Remote Similarity NPC38980
0.6438 Remote Similarity NPC303993
0.6435 Remote Similarity NPC204932
0.6434 Remote Similarity NPC150929
0.6434 Remote Similarity NPC41594
0.6429 Remote Similarity NPC214188
0.6429 Remote Similarity NPC74618
0.6429 Remote Similarity NPC105999
0.6429 Remote Similarity NPC301941
0.6424 Remote Similarity NPC184632
0.6424 Remote Similarity NPC225130
0.6423 Remote Similarity NPC117759
0.6423 Remote Similarity NPC281298
0.6423 Remote Similarity NPC310338
0.6419 Remote Similarity NPC224663
0.6408 Remote Similarity NPC134431
0.6408 Remote Similarity NPC156854
0.6408 Remote Similarity NPC191037
0.6408 Remote Similarity NPC178284
0.6408 Remote Similarity NPC304630
0.6408 Remote Similarity NPC58607
0.6408 Remote Similarity NPC17837
0.6389 Remote Similarity NPC474536
0.6383 Remote Similarity NPC48990
0.6383 Remote Similarity NPC114901
0.6383 Remote Similarity NPC293701
0.6377 Remote Similarity NPC61516
0.6377 Remote Similarity NPC227217
0.6377 Remote Similarity NPC247364
0.6377 Remote Similarity NPC117780
0.6377 Remote Similarity NPC232316
0.6377 Remote Similarity NPC474146
0.6377 Remote Similarity NPC95614
0.6377 Remote Similarity NPC56214
0.6377 Remote Similarity NPC10932
0.6377 Remote Similarity NPC165133
0.6377 Remote Similarity NPC242885
0.6377 Remote Similarity NPC232084
0.6364 Remote Similarity NPC319625
0.6364 Remote Similarity NPC111247
0.6364 Remote Similarity NPC50368
0.6364 Remote Similarity NPC147821
0.6364 Remote Similarity NPC163332
0.6364 Remote Similarity NPC292056
0.6364 Remote Similarity NPC41706
0.6364 Remote Similarity NPC183181
0.6364 Remote Similarity NPC210355
0.6364 Remote Similarity NPC470699
0.6364 Remote Similarity NPC471487
0.6364 Remote Similarity NPC118787
0.6358 Remote Similarity NPC474851
0.6358 Remote Similarity NPC118794
0.6358 Remote Similarity NPC474850
0.6357 Remote Similarity NPC296202
0.6349 Remote Similarity NPC307039
0.6349 Remote Similarity NPC132725
0.6331 Remote Similarity NPC207613
0.6331 Remote Similarity NPC189844
0.6331 Remote Similarity NPC109083

  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 NPC474375 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
0.7119 Intermediate Similarity NPD9296 Approved
0.6911 Remote Similarity NPD291 Approved
0.6723 Remote Similarity NPD9365 Approved
0.6691 Remote Similarity NPD915 Approved
0.6439 Remote Similarity NPD228 Approved
0.6434 Remote Similarity NPD968 Approved
0.6412 Remote Similarity NPD556 Approved
0.6281 Remote Similarity NPD9295 Approved
0.6279 Remote Similarity NPD9244 Approved
0.6207 Remote Similarity NPD1529 Clinical (unspecified phase)
0.6197 Remote Similarity NPD4379 Clinical (unspecified phase)
0.6176 Remote Similarity NPD9299 Approved
0.6154 Remote Similarity NPD9501 Approved
0.6149 Remote Similarity NPD1558 Phase 1
0.6138 Remote Similarity NPD1530 Clinical (unspecified phase)
0.6136 Remote Similarity NPD290 Approved
0.6136 Remote Similarity NPD9552 Approved
0.6066 Remote Similarity NPD9094 Approved
0.604 Remote Similarity NPD1613 Approved
0.604 Remote Similarity NPD1612 Clinical (unspecified phase)
0.5988 Remote Similarity NPD4010 Discontinued
0.597 Remote Similarity NPD2684 Approved
0.5957 Remote Similarity NPD1797 Approved
0.5957 Remote Similarity NPD1798 Approved
0.5946 Remote Similarity NPD3027 Phase 3
0.5915 Remote Similarity NPD2296 Approved
0.5887 Remote Similarity NPD1548 Phase 1
0.587 Remote Similarity NPD5283 Phase 1
0.5826 Remote Similarity NPD9087 Approved
0.5816 Remote Similarity NPD1408 Clinical (unspecified phase)
0.5816 Remote Similarity NPD1103 Approved
0.5816 Remote Similarity NPD1102 Approved
0.5804 Remote Similarity NPD6516 Phase 2
0.5804 Remote Similarity NPD5846 Approved
0.5797 Remote Similarity NPD7843 Approved
0.5786 Remote Similarity NPD6671 Approved
0.5763 Remote Similarity NPD9088 Approved
0.5734 Remote Similarity NPD1357 Approved
0.5724 Remote Similarity NPD1610 Phase 2
0.5724 Remote Similarity NPD1091 Approved
0.5724 Remote Similarity NPD1535 Discovery
0.5723 Remote Similarity NPD4288 Approved
0.5705 Remote Similarity NPD9494 Approved
0.5704 Remote Similarity NPD5536 Phase 2
0.5693 Remote Similarity NPD3021 Approved
0.5693 Remote Similarity NPD3022 Approved
0.5685 Remote Similarity NPD1481 Phase 2
0.5676 Remote Similarity NPD3827 Clinical (unspecified phase)
0.5676 Remote Similarity NPD1318 Phase 2
0.5674 Remote Similarity NPD7157 Approved
0.5674 Remote Similarity NPD191 Approved
0.5664 Remote Similarity NPD7533 Approved
0.5664 Remote Similarity NPD7534 Approved
0.5655 Remote Similarity NPD155 Clinical (unspecified phase)
0.5646 Remote Similarity NPD6582 Phase 2
0.5646 Remote Similarity NPD6583 Phase 3
0.563 Remote Similarity NPD9697 Approved
0.5621 Remote Similarity NPD3620 Phase 2
0.5621 Remote Similarity NPD3619 Clinical (unspecified phase)
0.5621 Remote Similarity NPD4060 Phase 1
0.56 Remote Similarity NPD2250 Discontinued

  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