Structure

Physi-Chem Properties

Molecular Weight:  525.71
Volume:  295.421
LogP:  6.486
LogD:  3.181
LogS:  -9.261
# Rotatable Bonds:  1
TPSA:  27.69
# H-Bond Aceptor:  3
# H-Bond Donor:  0
# Rings:  3
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.354
Synthetic Accessibility Score:  3.005
Fsp3:  0.077
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:  -4.862
MDCK Permeability:  1.645038355491124e-05
Pgp-inhibitor:  1.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.916
20% Bioavailability (F20%):  0.002
30% Bioavailability (F30%):  0.018

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.324
Plasma Protein Binding (PPB):  100.42386627197266%
Volume Distribution (VD):  2.288
Pgp-substrate:  6.558059215545654%

ADMET: Metabolism

CYP1A2-inhibitor:  0.958
CYP1A2-substrate:  0.195
CYP2C19-inhibitor:  0.835
CYP2C19-substrate:  0.518
CYP2C9-inhibitor:  0.874
CYP2C9-substrate:  0.883
CYP2D6-inhibitor:  0.003
CYP2D6-substrate:  0.84
CYP3A4-inhibitor:  0.165
CYP3A4-substrate:  0.214

ADMET: Excretion

Clearance (CL):  1.08
Half-life (T1/2):  0.128

ADMET: Toxicity

hERG Blockers:  0.036
Human Hepatotoxicity (H-HT):  0.138
Drug-inuced Liver Injury (DILI):  0.585
AMES Toxicity:  0.011
Rat Oral Acute Toxicity:  0.993
Maximum Recommended Daily Dose:  0.942
Skin Sensitization:  0.872
Carcinogencity:  0.222
Eye Corrosion:  0.036
Eye Irritation:  0.928
Respiratory Toxicity:  0.933

Download Data

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

  Natural Product: NPC163019

Natural Product ID:  NPC163019
Common Name*:   Spongiadioxin A Methyl Ether
IUPAC Name:   1,2,7,9-tetrabromo-4-methoxydibenzo-p-dioxin
Synonyms:   spongiadioxin A methyl ether
Standard InCHIKey:  FGKHPHARFIXFMH-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C13H6Br4O3/c1-18-8-4-6(15)10(17)13-12(8)19-9-3-5(14)2-7(16)11(9)20-13/h2-4H,1H3
SMILES:  COc1cc(Br)c(c2c1Oc1cc(Br)cc(c1O2)Br)Br
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL483851
PubChem CID:   10673765
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0002100] Benzodioxins
        • [CHEMONTID:0001379] Benzo-p-dioxins
          • [CHEMONTID:0001381] Dibenzo-p-dioxins

*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
NPO24471 Dysidea dendyi Species Dysideidae Eukaryota n.a. Australian n.a. PMID[11434317]
NPO24471 Dysidea dendyi Species Dysideidae Eukaryota n.a. n.a. n.a. PMID[12193037]
NPO24471 Dysidea dendyi Species Dysideidae 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 = 141000.0 nM PMID[536207]

☑ 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 NPC163019 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 NPC1744
0.9744 High Similarity NPC235166
0.9274 High Similarity NPC206183
0.9274 High Similarity NPC222684
0.92 High Similarity NPC178301
0.9068 High Similarity NPC264379
0.9032 High Similarity NPC45728
0.8917 High Similarity NPC71186
0.8898 High Similarity NPC221301
0.8824 High Similarity NPC162294
0.8629 High Similarity NPC173511
0.8629 High Similarity NPC88733
0.8492 Intermediate Similarity NPC131940
0.8492 Intermediate Similarity NPC81149
0.8492 Intermediate Similarity NPC230013
0.8492 Intermediate Similarity NPC68350
0.8492 Intermediate Similarity NPC197576
0.8468 Intermediate Similarity NPC41232
0.8468 Intermediate Similarity NPC63317
0.84 Intermediate Similarity NPC299939
0.84 Intermediate Similarity NPC170824
0.84 Intermediate Similarity NPC153580
0.84 Intermediate Similarity NPC226737
0.8333 Intermediate Similarity NPC40302
0.8333 Intermediate Similarity NPC137922
0.8306 Intermediate Similarity NPC104124
0.8268 Intermediate Similarity NPC25134
0.8268 Intermediate Similarity NPC159866
0.8268 Intermediate Similarity NPC295879
0.8268 Intermediate Similarity NPC97157
0.8268 Intermediate Similarity NPC64130
0.8268 Intermediate Similarity NPC175520
0.824 Intermediate Similarity NPC86007
0.824 Intermediate Similarity NPC44270
0.8189 Intermediate Similarity NPC474375
0.816 Intermediate Similarity NPC191194
0.8116 Intermediate Similarity NPC8577
0.8116 Intermediate Similarity NPC286337
0.811 Intermediate Similarity NPC196371
0.811 Intermediate Similarity NPC47769
0.7966 Intermediate Similarity NPC319933
0.72 Intermediate Similarity NPC152947
0.708 Intermediate Similarity NPC236265
0.7015 Intermediate Similarity NPC214289
0.6992 Remote Similarity NPC76915
0.6992 Remote Similarity NPC151617
0.6984 Remote Similarity NPC307875
0.6949 Remote Similarity NPC47422
0.6929 Remote Similarity NPC232654
0.6912 Remote Similarity NPC472596
0.6912 Remote Similarity NPC205850
0.6891 Remote Similarity NPC302546
0.6828 Remote Similarity NPC245386
0.6812 Remote Similarity NPC126216
0.6812 Remote Similarity NPC105147
0.6812 Remote Similarity NPC261661
0.6812 Remote Similarity NPC228875
0.6803 Remote Similarity NPC271942
0.6791 Remote Similarity NPC123948
0.6788 Remote Similarity NPC276195
0.6769 Remote Similarity NPC165386
0.6763 Remote Similarity NPC217854
0.6761 Remote Similarity NPC31707
0.6761 Remote Similarity NPC247146
0.6744 Remote Similarity NPC124712
0.6739 Remote Similarity NPC145780
0.6738 Remote Similarity NPC244364
0.6723 Remote Similarity NPC206876
0.6714 Remote Similarity NPC25817
0.6691 Remote Similarity NPC152722
0.6667 Remote Similarity NPC160081
0.6667 Remote Similarity NPC226493
0.6667 Remote Similarity NPC203924
0.6643 Remote Similarity NPC192810
0.6642 Remote Similarity NPC475961
0.6642 Remote Similarity NPC254625
0.6642 Remote Similarity NPC15805
0.6621 Remote Similarity NPC469698
0.6621 Remote Similarity NPC473412
0.662 Remote Similarity NPC189589
0.662 Remote Similarity NPC298845
0.662 Remote Similarity NPC469622
0.662 Remote Similarity NPC110677
0.6597 Remote Similarity NPC85049
0.6597 Remote Similarity NPC474227
0.6596 Remote Similarity NPC221090
0.6575 Remote Similarity NPC202762
0.6575 Remote Similarity NPC86655
0.6575 Remote Similarity NPC127624
0.6573 Remote Similarity NPC474119
0.6573 Remote Similarity NPC216836
0.6573 Remote Similarity NPC37074
0.6573 Remote Similarity NPC210355
0.6573 Remote Similarity NPC194841
0.6571 Remote Similarity NPC194626
0.6567 Remote Similarity NPC204120
0.6558 Remote Similarity NPC113862
0.6556 Remote Similarity NPC89341
0.6547 Remote Similarity NPC199023
0.6547 Remote Similarity NPC166759
0.6541 Remote Similarity NPC255068
0.6538 Remote Similarity NPC473653
0.6533 Remote Similarity NPC160932
0.6532 Remote Similarity NPC16649
0.6531 Remote Similarity NPC263064
0.6531 Remote Similarity NPC244890
0.6528 Remote Similarity NPC474651
0.6528 Remote Similarity NPC474623
0.6528 Remote Similarity NPC63179
0.6528 Remote Similarity NPC210674
0.6522 Remote Similarity NPC59561
0.6522 Remote Similarity NPC172253
0.6519 Remote Similarity NPC135103
0.6507 Remote Similarity NPC474238
0.6503 Remote Similarity NPC171533
0.65 Remote Similarity NPC477886
0.65 Remote Similarity NPC75713
0.6489 Remote Similarity NPC35543
0.6486 Remote Similarity NPC170694
0.6486 Remote Similarity NPC317380
0.6486 Remote Similarity NPC474478
0.6483 Remote Similarity NPC285339
0.6483 Remote Similarity NPC222004
0.6483 Remote Similarity NPC210623
0.6483 Remote Similarity NPC226788
0.6483 Remote Similarity NPC202582
0.6483 Remote Similarity NPC3439
0.6483 Remote Similarity NPC45824
0.6483 Remote Similarity NPC273295
0.6483 Remote Similarity NPC470258
0.6483 Remote Similarity NPC190629
0.6483 Remote Similarity NPC218856
0.6479 Remote Similarity NPC122792
0.6479 Remote Similarity NPC228972
0.6475 Remote Similarity NPC474565
0.6475 Remote Similarity NPC10932
0.6475 Remote Similarity NPC247364
0.6475 Remote Similarity NPC232084
0.6475 Remote Similarity NPC61516
0.6471 Remote Similarity NPC125306
0.6466 Remote Similarity NPC247871
0.6466 Remote Similarity NPC106141
0.6463 Remote Similarity NPC303011
0.646 Remote Similarity NPC475697
0.6458 Remote Similarity NPC5447
0.6458 Remote Similarity NPC469621
0.6458 Remote Similarity NPC250432
0.6457 Remote Similarity NPC314803
0.6454 Remote Similarity NPC473411
0.6454 Remote Similarity NPC262253
0.6454 Remote Similarity NPC71579
0.6449 Remote Similarity NPC228907
0.6447 Remote Similarity NPC118794
0.6443 Remote Similarity NPC470356
0.6443 Remote Similarity NPC94750
0.6443 Remote Similarity NPC234333
0.6443 Remote Similarity NPC195022
0.6443 Remote Similarity NPC260898
0.6443 Remote Similarity NPC311430
0.6443 Remote Similarity NPC121812
0.6443 Remote Similarity NPC112246
0.6443 Remote Similarity NPC47398
0.6443 Remote Similarity NPC474206
0.6443 Remote Similarity NPC112939
0.6443 Remote Similarity NPC61946
0.6443 Remote Similarity NPC224941
0.6439 Remote Similarity NPC245115
0.6438 Remote Similarity NPC214860
0.6438 Remote Similarity NPC79184
0.6438 Remote Similarity NPC469614
0.6438 Remote Similarity NPC307042
0.6438 Remote Similarity NPC60756
0.6438 Remote Similarity NPC208769
0.6438 Remote Similarity NPC91291
0.6438 Remote Similarity NPC472338
0.6438 Remote Similarity NPC229231
0.6438 Remote Similarity NPC469612
0.6438 Remote Similarity NPC476399
0.6429 Remote Similarity NPC109346
0.6429 Remote Similarity NPC471486
0.6423 Remote Similarity NPC193067
0.642 Remote Similarity NPC38980
0.6419 Remote Similarity NPC36661
0.6419 Remote Similarity NPC168059
0.6419 Remote Similarity NPC229442
0.6414 Remote Similarity NPC226331
0.6414 Remote Similarity NPC46274
0.6408 Remote Similarity NPC474169
0.6408 Remote Similarity NPC282496
0.6408 Remote Similarity NPC95168
0.6408 Remote Similarity NPC108545
0.6408 Remote Similarity NPC233526
0.6408 Remote Similarity NPC473572
0.6403 Remote Similarity NPC226629
0.64 Remote Similarity NPC173660
0.64 Remote Similarity NPC474639
0.64 Remote Similarity NPC78047
0.64 Remote Similarity NPC306441
0.64 Remote Similarity NPC162659
0.64 Remote Similarity NPC270456

  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 NPC163019 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
0.6992 Remote Similarity NPD1408 Clinical (unspecified phase)
0.6761 Remote Similarity NPD3537 Clinical (unspecified phase)
0.6691 Remote Similarity NPD7534 Approved
0.6691 Remote Similarity NPD7533 Approved
0.6614 Remote Similarity NPD291 Approved
0.6458 Remote Similarity NPD1530 Clinical (unspecified phase)
0.6454 Remote Similarity NPD2981 Phase 2
0.6414 Remote Similarity NPD1529 Clinical (unspecified phase)
0.6408 Remote Similarity NPD2982 Phase 2
0.6408 Remote Similarity NPD2983 Phase 2
0.6351 Remote Similarity NPD1613 Approved
0.6351 Remote Similarity NPD1612 Clinical (unspecified phase)
0.6331 Remote Similarity NPD1548 Phase 1
0.629 Remote Similarity NPD9365 Approved
0.627 Remote Similarity NPD9296 Approved
0.6269 Remote Similarity NPD556 Approved
0.6268 Remote Similarity NPD1610 Phase 2
0.625 Remote Similarity NPD3454 Phase 3
0.6233 Remote Similarity NPD3018 Phase 2
0.6196 Remote Similarity NPD4288 Approved
0.6149 Remote Similarity NPD3027 Phase 3
0.6099 Remote Similarity NPD8095 Phase 1
0.6081 Remote Similarity NPD4908 Phase 1
0.6054 Remote Similarity NPD1469 Clinical (unspecified phase)
0.6028 Remote Similarity NPD1102 Approved
0.6028 Remote Similarity NPD1103 Approved
0.6 Remote Similarity NPD4907 Clinical (unspecified phase)
0.5971 Remote Similarity NPD5283 Phase 1
0.5959 Remote Similarity NPD4749 Approved
0.5933 Remote Similarity NPD4625 Phase 3
0.592 Remote Similarity NPD9094 Approved
0.5882 Remote Similarity NPD290 Approved
0.5882 Remote Similarity NPD1933 Approved
0.5833 Remote Similarity NPD3539 Phase 1
0.5822 Remote Similarity NPD1091 Approved
0.5822 Remote Similarity NPD422 Phase 1
0.5809 Remote Similarity NPD968 Approved
0.5804 Remote Similarity NPD5536 Phase 2
0.5802 Remote Similarity NPD2184 Approved
0.5802 Remote Similarity NPD2183 Approved
0.5796 Remote Similarity NPD3540 Phase 1
0.5789 Remote Similarity NPD6410 Clinical (unspecified phase)
0.5789 Remote Similarity NPD6859 Clinical (unspecified phase)
0.5783 Remote Similarity NPD1934 Approved
0.5778 Remote Similarity NPD9501 Approved
0.5766 Remote Similarity NPD9552 Approved
0.5753 Remote Similarity NPD155 Clinical (unspecified phase)
0.5753 Remote Similarity NPD915 Approved
0.5752 Remote Similarity NPD3531 Approved
0.5752 Remote Similarity NPD3532 Approved
0.5752 Remote Similarity NPD3530 Approved
0.575 Remote Similarity NPD5307 Clinical (unspecified phase)
0.5748 Remote Similarity NPD9295 Approved
0.5746 Remote Similarity NPD4287 Approved
0.5738 Remote Similarity NPD9093 Approved
0.5725 Remote Similarity NPD2684 Approved
0.5724 Remote Similarity NPD1798 Approved
0.5724 Remote Similarity NPD1797 Approved
0.5714 Remote Similarity NPD1558 Phase 1
0.5714 Remote Similarity NPD228 Approved
0.5714 Remote Similarity NPD3705 Approved
0.5706 Remote Similarity NPD1940 Clinical (unspecified phase)
0.5698 Remote Similarity NPD4010 Discontinued
0.5697 Remote Similarity NPD6055 Clinical (unspecified phase)
0.5691 Remote Similarity NPD9089 Approved
0.5689 Remote Similarity NPD3384 Approved
0.5689 Remote Similarity NPD3383 Approved
0.5689 Remote Similarity NPD3382 Approved
0.5674 Remote Similarity NPD5535 Approved
0.5667 Remote Similarity NPD1318 Phase 2
0.5665 Remote Similarity NPD6688 Approved
0.5665 Remote Similarity NPD6687 Approved
0.5663 Remote Similarity NPD1009 Approved
0.5663 Remote Similarity NPD4678 Approved
0.5663 Remote Similarity NPD4675 Approved
0.5662 Remote Similarity NPD9244 Approved
0.5658 Remote Similarity NPD5752 Clinical (unspecified phase)
0.5655 Remote Similarity NPD2801 Approved
0.5643 Remote Similarity NPD2671 Approved
0.5643 Remote Similarity NPD2673 Approved
0.5636 Remote Similarity NPD1653 Approved
0.5633 Remote Similarity NPD2796 Approved
0.5625 Remote Similarity NPD1652 Phase 2
0.5621 Remote Similarity NPD3817 Phase 2
0.5617 Remote Similarity NPD7124 Phase 2
0.5605 Remote Similarity NPD6111 Discontinued
0.5605 Remote Similarity NPD2200 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