Structure

Physi-Chem Properties

Molecular Weight:  729.55
Volume:  377.421
LogP:  6.178
LogD:  2.724
LogS:  -3.553
# Rotatable Bonds:  4
TPSA:  90.15
# H-Bond Aceptor:  5
# H-Bond Donor:  4
# Rings:  2
# Heavy Atoms:  11

MedChem Properties

QED Drug-Likeness Score:  0.205
Synthetic Accessibility Score:  3.247
Fsp3:  0.143
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  4
Golden Triangle Rule:  Rejected
Chelating Alert:  1
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.99
MDCK Permeability:  1.6429588868049905e-05
Pgp-inhibitor:  0.999
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.987
20% Bioavailability (F20%):  0.036
30% Bioavailability (F30%):  0.102

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.213
Plasma Protein Binding (PPB):  103.04874420166016%
Volume Distribution (VD):  2.661
Pgp-substrate:  2.9466278553009033%

ADMET: Metabolism

CYP1A2-inhibitor:  0.485
CYP1A2-substrate:  0.235
CYP2C19-inhibitor:  0.068
CYP2C19-substrate:  0.059
CYP2C9-inhibitor:  0.841
CYP2C9-substrate:  0.246
CYP2D6-inhibitor:  0.001
CYP2D6-substrate:  0.145
CYP3A4-inhibitor:  0.04
CYP3A4-substrate:  0.067

ADMET: Excretion

Clearance (CL):  0.486
Half-life (T1/2):  0.857

ADMET: Toxicity

hERG Blockers:  0.126
Human Hepatotoxicity (H-HT):  0.177
Drug-inuced Liver Injury (DILI):  0.936
AMES Toxicity:  0.025
Rat Oral Acute Toxicity:  0.39
Maximum Recommended Daily Dose:  0.012
Skin Sensitization:  0.954
Carcinogencity:  0.031
Eye Corrosion:  0.004
Eye Irritation:  0.91
Respiratory Toxicity:  0.193

Download Data

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

  Natural Product: NPC303011

Natural Product ID:  NPC303011
Common Name*:   4-((2,3,6-Tribromo-4,5-Dihydroxybenzyloxy)Methyl)-3,5,6-Tribromobenzene-1,2-Diol
IUPAC Name:   3,4,6-tribromo-5-[(2,3,6-tribromo-4,5-dihydroxyphenyl)methoxymethyl]benzene-1,2-diol
Synonyms:  
Standard InCHIKey:  BRLKFLGNILMDCZ-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C14H8Br6O5/c15-5-3(7(17)11(21)13(23)9(5)19)1-25-2-4-6(16)10(20)14(24)12(22)8(4)18/h21-24H,1-2H2
SMILES:  Brc1c(COCc2c(Br)c(O)c(c(c2Br)Br)O)c(Br)c(c(c1O)O)Br
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL228430
PubChem CID:   23426771
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0002448] Benzenoids
      • [CHEMONTID:0002279] Benzene and substituted derivatives
        • [CHEMONTID:0002542] Benzylethers

*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 = 8500.0 nM PMID[508829]

☑ 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 NPC303011 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
0.9615 High Similarity NPC271942
0.9466 High Similarity NPC168680
0.9365 High Similarity NPC134219
0.9237 High Similarity NPC245386
0.8976 High Similarity NPC84606
0.8898 High Similarity NPC219444
0.8889 High Similarity NPC227976
0.8788 High Similarity NPC226493
0.8788 High Similarity NPC160081
0.8712 High Similarity NPC85049
0.8702 High Similarity NPC474147
0.8702 High Similarity NPC473708
0.8696 High Similarity NPC89341
0.8686 High Similarity NPC160932
0.8626 High Similarity NPC43706
0.8561 High Similarity NPC13004
0.8511 High Similarity NPC109346
0.8413 Intermediate Similarity NPC50782
0.8345 Intermediate Similarity NPC156356
0.8321 Intermediate Similarity NPC163560
0.8271 Intermediate Similarity NPC220311
0.8258 Intermediate Similarity NPC474169
0.8258 Intermediate Similarity NPC473572
0.8219 Intermediate Similarity NPC152947
0.8195 Intermediate Similarity NPC137117
0.8182 Intermediate Similarity NPC229213
0.8182 Intermediate Similarity NPC47790
0.8162 Intermediate Similarity NPC105702
0.8092 Intermediate Similarity NPC474146
0.8088 Intermediate Similarity NPC150929
0.8029 Intermediate Similarity NPC474614
0.8014 Intermediate Similarity NPC224663
0.7929 Intermediate Similarity NPC244890
0.7826 Intermediate Similarity NPC55113
0.7744 Intermediate Similarity NPC38483
0.7671 Intermediate Similarity NPC118794
0.7652 Intermediate Similarity NPC79844
0.7606 Intermediate Similarity NPC300678
0.7574 Intermediate Similarity NPC136543
0.7535 Intermediate Similarity NPC110800
0.75 Intermediate Similarity NPC475697
0.75 Intermediate Similarity NPC7398
0.7482 Intermediate Similarity NPC142776
0.7436 Intermediate Similarity NPC474535
0.7417 Intermediate Similarity NPC113862
0.7379 Intermediate Similarity NPC312155
0.7303 Intermediate Similarity NPC88896
0.7273 Intermediate Similarity NPC474536
0.7214 Intermediate Similarity NPC68350
0.7214 Intermediate Similarity NPC230013
0.7214 Intermediate Similarity NPC197576
0.7214 Intermediate Similarity NPC81149
0.7214 Intermediate Similarity NPC131940
0.7194 Intermediate Similarity NPC40302
0.7194 Intermediate Similarity NPC474375
0.7194 Intermediate Similarity NPC137922
0.7192 Intermediate Similarity NPC471328
0.7172 Intermediate Similarity NPC43613
0.7164 Intermediate Similarity NPC471488
0.7143 Intermediate Similarity NPC25134
0.7143 Intermediate Similarity NPC175520
0.7143 Intermediate Similarity NPC97157
0.7143 Intermediate Similarity NPC159866
0.7143 Intermediate Similarity NPC64130
0.7143 Intermediate Similarity NPC295879
0.7134 Intermediate Similarity NPC135103
0.7125 Intermediate Similarity NPC38980
0.7122 Intermediate Similarity NPC471486
0.7121 Intermediate Similarity NPC54543
0.7071 Intermediate Similarity NPC88733
0.7071 Intermediate Similarity NPC173511
0.705 Intermediate Similarity NPC41232
0.705 Intermediate Similarity NPC63317
0.704 Intermediate Similarity NPC475466
0.7039 Intermediate Similarity NPC184632
0.7 Intermediate Similarity NPC170824
0.7 Intermediate Similarity NPC153580
0.7 Intermediate Similarity NPC196371
0.7 Intermediate Similarity NPC226737
0.7 Intermediate Similarity NPC47769
0.7 Intermediate Similarity NPC299939
0.7 Intermediate Similarity NPC470414
0.6987 Remote Similarity NPC473608
0.6986 Remote Similarity NPC178301
0.698 Remote Similarity NPC199089
0.6978 Remote Similarity NPC117759
0.6972 Remote Similarity NPC105999
0.694 Remote Similarity NPC473358
0.6923 Remote Similarity NPC236265
0.6918 Remote Similarity NPC206183
0.6918 Remote Similarity NPC222684
0.6912 Remote Similarity NPC33244
0.6906 Remote Similarity NPC104124
0.6892 Remote Similarity NPC474135
0.6879 Remote Similarity NPC226514
0.6857 Remote Similarity NPC86007
0.6857 Remote Similarity NPC44270
0.6853 Remote Similarity NPC473451
0.6815 Remote Similarity NPC178097
0.6806 Remote Similarity NPC131747
0.6806 Remote Similarity NPC257682
0.6806 Remote Similarity NPC146355
0.6806 Remote Similarity NPC213414
0.6791 Remote Similarity NPC471495
0.6786 Remote Similarity NPC191194
0.6786 Remote Similarity NPC71186
0.6757 Remote Similarity NPC11449
0.6748 Remote Similarity NPC305490
0.6739 Remote Similarity NPC94217
0.6713 Remote Similarity NPC147654
0.6712 Remote Similarity NPC45728
0.6712 Remote Similarity NPC178284
0.6712 Remote Similarity NPC58607
0.6712 Remote Similarity NPC191037
0.6691 Remote Similarity NPC471487
0.6667 Remote Similarity NPC292056
0.6667 Remote Similarity NPC471485
0.6667 Remote Similarity NPC183181
0.6667 Remote Similarity NPC275519
0.6667 Remote Similarity NPC41706
0.6667 Remote Similarity NPC319625
0.6667 Remote Similarity NPC118787
0.6667 Remote Similarity NPC111247
0.6667 Remote Similarity NPC147821
0.6667 Remote Similarity NPC294870
0.6667 Remote Similarity NPC296202
0.6667 Remote Similarity NPC163332
0.6644 Remote Similarity NPC194519
0.6643 Remote Similarity NPC264379
0.6629 Remote Similarity NPC471591
0.6622 Remote Similarity NPC72529
0.6622 Remote Similarity NPC282703
0.6622 Remote Similarity NPC45774
0.6622 Remote Similarity NPC184733
0.6622 Remote Similarity NPC245826
0.6622 Remote Similarity NPC128208
0.6622 Remote Similarity NPC129570
0.6622 Remote Similarity NPC21867
0.6622 Remote Similarity NPC474178
0.6622 Remote Similarity NPC252307
0.6622 Remote Similarity NPC11258
0.6621 Remote Similarity NPC212541
0.6621 Remote Similarity NPC471693
0.662 Remote Similarity NPC226629
0.662 Remote Similarity NPC477803
0.662 Remote Similarity NPC320987
0.662 Remote Similarity NPC181969
0.6618 Remote Similarity NPC473372
0.6603 Remote Similarity NPC79076
0.66 Remote Similarity NPC158078
0.6597 Remote Similarity NPC7830
0.6597 Remote Similarity NPC470804
0.6591 Remote Similarity NPC473409
0.6591 Remote Similarity NPC82741
0.6591 Remote Similarity NPC141405
0.6577 Remote Similarity NPC478071
0.6577 Remote Similarity NPC5851
0.6577 Remote Similarity NPC86030
0.6575 Remote Similarity NPC109822
0.6575 Remote Similarity NPC94276
0.6573 Remote Similarity NPC35071
0.6573 Remote Similarity NPC177475
0.6573 Remote Similarity NPC148615
0.6573 Remote Similarity NPC180207
0.6554 Remote Similarity NPC118533
0.6554 Remote Similarity NPC165045
0.6554 Remote Similarity NPC122359
0.6554 Remote Similarity NPC5428
0.6554 Remote Similarity NPC78061
0.6554 Remote Similarity NPC159987
0.6552 Remote Similarity NPC209567
0.6549 Remote Similarity NPC255675
0.6547 Remote Similarity NPC264558
0.6538 Remote Similarity NPC8577
0.6538 Remote Similarity NPC250597
0.6533 Remote Similarity NPC242807
0.6533 Remote Similarity NPC241522
0.6533 Remote Similarity NPC187998
0.6533 Remote Similarity NPC42300
0.6533 Remote Similarity NPC174495
0.6533 Remote Similarity NPC145305
0.6533 Remote Similarity NPC153739
0.6533 Remote Similarity NPC64201
0.6533 Remote Similarity NPC92164
0.6533 Remote Similarity NPC257582
0.6533 Remote Similarity NPC77040
0.6531 Remote Similarity NPC148627
0.6529 Remote Similarity NPC288747
0.6525 Remote Similarity NPC221049
0.6515 Remote Similarity NPC223393
0.651 Remote Similarity NPC472968
0.651 Remote Similarity NPC214553
0.6507 Remote Similarity NPC136319
0.6507 Remote Similarity NPC84086
0.6503 Remote Similarity NPC141791
0.6503 Remote Similarity NPC263386
0.65 Remote Similarity NPC221301
0.65 Remote Similarity NPC120280
0.6494 Remote Similarity NPC213471
0.6493 Remote Similarity NPC471511

  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 NPC303011 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
0.6742 Remote Similarity NPD9244 Approved
0.6467 Remote Similarity NPD3027 Phase 3
0.6447 Remote Similarity NPD1612 Clinical (unspecified phase)
0.6447 Remote Similarity NPD1613 Approved
0.6443 Remote Similarity NPD1530 Clinical (unspecified phase)
0.64 Remote Similarity NPD1529 Clinical (unspecified phase)
0.6286 Remote Similarity NPD228 Approved
0.6259 Remote Similarity NPD3021 Approved
0.6259 Remote Similarity NPD3022 Approved
0.6257 Remote Similarity NPD4010 Discontinued
0.6101 Remote Similarity NPD7266 Discontinued
0.6101 Remote Similarity NPD2029 Clinical (unspecified phase)
0.609 Remote Similarity NPD230 Phase 1
0.6067 Remote Similarity NPD4379 Clinical (unspecified phase)
0.6026 Remote Similarity NPD1558 Phase 1
0.5986 Remote Similarity NPD9280 Clinical (unspecified phase)
0.5951 Remote Similarity NPD6190 Approved
0.5929 Remote Similarity NPD968 Approved
0.5912 Remote Similarity NPD1242 Phase 1
0.5909 Remote Similarity NPD2861 Phase 2
0.5906 Remote Similarity NPD9381 Approved
0.5906 Remote Similarity NPD9384 Approved
0.5906 Remote Similarity NPD4288 Approved
0.5878 Remote Similarity NPD1548 Phase 1
0.5862 Remote Similarity NPD5283 Phase 1
0.5828 Remote Similarity NPD3705 Approved
0.5828 Remote Similarity NPD1610 Phase 2
0.5823 Remote Similarity NPD3061 Approved
0.5823 Remote Similarity NPD3059 Approved
0.5823 Remote Similarity NPD3062 Approved
0.5783 Remote Similarity NPD1511 Approved
0.5776 Remote Similarity NPD1169 Approved
0.5752 Remote Similarity NPD9622 Approved
0.5752 Remote Similarity NPD2982 Phase 2
0.5752 Remote Similarity NPD2983 Phase 2
0.575 Remote Similarity NPD5314 Approved
0.5749 Remote Similarity NPD4160 Clinical (unspecified phase)
0.5732 Remote Similarity NPD9718 Approved
0.5723 Remote Similarity NPD3619 Clinical (unspecified phase)
0.5723 Remote Similarity NPD3620 Phase 2
0.5723 Remote Similarity NPD2296 Approved
0.5714 Remote Similarity NPD1512 Approved
0.5705 Remote Similarity NPD3018 Phase 2
0.5698 Remote Similarity NPD1934 Approved
0.5686 Remote Similarity NPD2981 Phase 2
0.5685 Remote Similarity NPD9377 Approved
0.5685 Remote Similarity NPD9379 Approved
0.5674 Remote Similarity NPD6688 Approved
0.5674 Remote Similarity NPD6687 Approved
0.5669 Remote Similarity NPD4908 Phase 1
0.5668 Remote Similarity NPD4287 Approved
0.5665 Remote Similarity NPD2393 Clinical (unspecified phase)
0.5662 Remote Similarity NPD2934 Approved
0.5662 Remote Similarity NPD2933 Approved
0.5655 Remote Similarity NPD4123 Phase 3
0.5647 Remote Similarity NPD1653 Approved
0.5641 Remote Similarity NPD9619 Approved
0.5641 Remote Similarity NPD9620 Approved
0.5641 Remote Similarity NPD9621 Approved
0.5636 Remote Similarity NPD3060 Approved
0.5636 Remote Similarity NPD6674 Discontinued
0.5629 Remote Similarity NPD1357 Approved
0.5625 Remote Similarity NPD4060 Phase 1
0.5621 Remote Similarity NPD1091 Approved
0.562 Remote Similarity NPD2859 Approved
0.562 Remote Similarity NPD2860 Approved
0.5612 Remote Similarity NPD3020 Approved
0.5605 Remote Similarity NPD9494 Approved
0.56 Remote Similarity NPD4868 Clinical (unspecified phase)
0.56 Remote Similarity NPD5536 Phase 2

  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