NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	511.69
Volume:	278.125
LogP:	6.288
LogD:	2.771
LogS:	-8.786
# Rotatable Bonds:	0
TPSA:	38.69
# H-Bond Aceptor:	3
# H-Bond Donor:	1
# Rings:	3
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.38
Synthetic Accessibility Score:	3.182
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:	-4.873
MDCK Permeability:	1.6562968085054308e-05
Pgp-inhibitor:	1.0
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.958
20% Bioavailability (F20%):	0.005
30% Bioavailability (F30%):	0.007

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.255
Plasma Protein Binding (PPB):	101.25359344482422%
Volume Distribution (VD):	1.736
Pgp-substrate:	5.237928867340088%

ADMET: Metabolism

CYP1A2-inhibitor:	0.965
CYP1A2-substrate:	0.156
CYP2C19-inhibitor:	0.761
CYP2C19-substrate:	0.155
CYP2C9-inhibitor:	0.801
CYP2C9-substrate:	0.752
CYP2D6-inhibitor:	0.012
CYP2D6-substrate:	0.583
CYP3A4-inhibitor:	0.09
CYP3A4-substrate:	0.143

ADMET: Excretion

Clearance (CL):	0.89
Half-life (T1/2):	0.172

ADMET: Toxicity

hERG Blockers:	0.032
Human Hepatotoxicity (H-HT):	0.194
Drug-inuced Liver Injury (DILI):	0.401
AMES Toxicity:	0.011
Rat Oral Acute Toxicity:	0.99
Maximum Recommended Daily Dose:	0.942
Skin Sensitization:	0.789
Carcinogencity:	0.365
Eye Corrosion:	0.023
Eye Irritation:	0.946
Respiratory Toxicity:	0.955

Download Data

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

Natural Product: NPC206183

Natural Product ID:	NPC206183
*Common Name:**	Spongiadioxin B
IUPAC Name:	2,3,6,8-tetrabromodibenzo-p-dioxin-1-ol
Synonyms:
Standard InCHIKey:	OKZDDAYLOUDZAH-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C12H4Br4O3/c13-4-1-6(15)11-7(2-4)19-12-8(18-11)3-5(14)9(16)10(12)17/h1-3,17H
SMILES:	Brc1cc2Oc3c(Oc2c(c1)Br)cc(c(c3O)Br)Br
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL470276
PubChem CID:	10459177
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

Activity Type	# Activity
ED50	1
IC50	1
LD50	1

Activity Type	# Activity
NON-MOLECULAR	1
Organism	1
Others	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	ED50	=	15.5	ug ml-1	PMID[505612]
NPT32	Organism	Mus musculus	Mus musculus	LD50	>	150.0	mg.kg-1	PMID[505612]
NPT2	Others	Unspecified		IC50	=	1100.0	nM	PMID[505613]

☑ 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 NPC206183 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	1003
0.1-0.2	6698
0.2-0.3	14230
0.3-0.4	4722
0.4-0.5	7400
0.5-0.6	7431
0.6-0.7	1136
0.7-0.8	26
0.8-0.85	9
0.85-0.9	15
0.9-0.95	23
0.95-1	4

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC222684
0.9754	High Similarity	NPC45728
0.96	High Similarity	NPC178301
0.9274	High Similarity	NPC163019
0.9274	High Similarity	NPC1744
0.918	High Similarity	NPC41232
0.918	High Similarity	NPC63317
0.9106	High Similarity	NPC226737
0.9106	High Similarity	NPC153580
0.9106	High Similarity	NPC299939
0.9032	High Similarity	NPC235166
0.9032	High Similarity	NPC88733
0.9032	High Similarity	NPC137922
0.9032	High Similarity	NPC40302
0.9032	High Similarity	NPC173511
0.9016	High Similarity	NPC104124
0.896	High Similarity	NPC64130
0.896	High Similarity	NPC159866
0.896	High Similarity	NPC175520
0.896	High Similarity	NPC295879
0.896	High Similarity	NPC97157
0.896	High Similarity	NPC25134
0.8943	High Similarity	NPC44270
0.8943	High Similarity	NPC86007
0.8889	High Similarity	NPC68350
0.8889	High Similarity	NPC197576
0.8889	High Similarity	NPC131940
0.8889	High Similarity	NPC81149
0.8889	High Similarity	NPC230013
0.888	High Similarity	NPC474375
0.8862	High Similarity	NPC191194
0.88	High Similarity	NPC196371
0.88	High Similarity	NPC47769
0.88	High Similarity	NPC170824
0.875	High Similarity	NPC8577
0.84	Intermediate Similarity	NPC264379
0.8268	Intermediate Similarity	NPC71186
0.824	Intermediate Similarity	NPC221301
0.8175	Intermediate Similarity	NPC162294
0.7958	Intermediate Similarity	NPC286337
0.7652	Intermediate Similarity	NPC214289
0.7651	Intermediate Similarity	NPC152947
0.7642	Intermediate Similarity	NPC319933
0.7634	Intermediate Similarity	NPC76915
0.7634	Intermediate Similarity	NPC151617
0.7537	Intermediate Similarity	NPC205850
0.7426	Intermediate Similarity	NPC228875
0.7426	Intermediate Similarity	NPC126216
0.7426	Intermediate Similarity	NPC105147
0.7381	Intermediate Similarity	NPC307875
0.7292	Intermediate Similarity	NPC245386
0.726	Intermediate Similarity	NPC271942
0.7226	Intermediate Similarity	NPC145780
0.7214	Intermediate Similarity	NPC110677
0.7132	Intermediate Similarity	NPC124712
0.7103	Intermediate Similarity	NPC244890
0.7071	Intermediate Similarity	NPC122792
0.7071	Intermediate Similarity	NPC228972
0.7054	Intermediate Similarity	NPC232654
0.7042	Intermediate Similarity	NPC5447
0.7042	Intermediate Similarity	NPC250432
0.7014	Intermediate Similarity	NPC160081
0.7014	Intermediate Similarity	NPC226493
0.7	Intermediate Similarity	NPC118794
0.7	Intermediate Similarity	NPC192810
0.6993	Remote Similarity	NPC226331
0.6993	Remote Similarity	NPC46274
0.6984	Remote Similarity	NPC314803
0.6972	Remote Similarity	NPC189589
0.6972	Remote Similarity	NPC469622
0.6972	Remote Similarity	NPC181361
0.695	Remote Similarity	NPC221090
0.6944	Remote Similarity	NPC85049
0.6935	Remote Similarity	NPC475466
0.6929	Remote Similarity	NPC152722
0.6923	Remote Similarity	NPC210355
0.6923	Remote Similarity	NPC37074
0.6923	Remote Similarity	NPC216836
0.6923	Remote Similarity	NPC470699
0.6918	Remote Similarity	NPC202762
0.6918	Remote Similarity	NPC86655
0.6918	Remote Similarity	NPC303011
0.6918	Remote Similarity	NPC127624
0.6897	Remote Similarity	NPC91291
0.6887	Remote Similarity	NPC89341
0.6867	Remote Similarity	NPC160932
0.6861	Remote Similarity	NPC9248
0.6857	Remote Similarity	NPC190454
0.6857	Remote Similarity	NPC97432
0.6853	Remote Similarity	NPC298845
0.6849	Remote Similarity	NPC268342
0.6849	Remote Similarity	NPC42760
0.6849	Remote Similarity	NPC220825
0.6849	Remote Similarity	NPC268266
0.6835	Remote Similarity	NPC61516
0.6835	Remote Similarity	NPC232084
0.6835	Remote Similarity	NPC10932
0.6835	Remote Similarity	NPC247364
0.6828	Remote Similarity	NPC45824
0.6824	Remote Similarity	NPC317380
0.6824	Remote Similarity	NPC170694
0.6809	Remote Similarity	NPC71579
0.6809	Remote Similarity	NPC262253
0.6809	Remote Similarity	NPC473411
0.6806	Remote Similarity	NPC469621
0.6806	Remote Similarity	NPC50368
0.6806	Remote Similarity	NPC13004
0.6803	Remote Similarity	NPC15658
0.6803	Remote Similarity	NPC261619
0.6803	Remote Similarity	NPC78770
0.6803	Remote Similarity	NPC61477
0.6803	Remote Similarity	NPC126029
0.6803	Remote Similarity	NPC185604
0.6803	Remote Similarity	NPC474134
0.6803	Remote Similarity	NPC219876
0.6803	Remote Similarity	NPC131128
0.6791	Remote Similarity	NPC255068
0.6788	Remote Similarity	NPC193067
0.6786	Remote Similarity	NPC471486
0.6786	Remote Similarity	NPC276195
0.6783	Remote Similarity	NPC220311
0.6781	Remote Similarity	NPC214860
0.6781	Remote Similarity	NPC208769
0.6781	Remote Similarity	NPC472338
0.6779	Remote Similarity	NPC112246
0.6779	Remote Similarity	NPC234333
0.6779	Remote Similarity	NPC260898
0.6779	Remote Similarity	NPC470356
0.6779	Remote Similarity	NPC94750
0.6779	Remote Similarity	NPC47398
0.6779	Remote Similarity	NPC112939
0.6779	Remote Similarity	NPC121812
0.6779	Remote Similarity	NPC474206
0.677	Remote Similarity	NPC475697
0.6763	Remote Similarity	NPC226629
0.6761	Remote Similarity	NPC95168
0.6761	Remote Similarity	NPC474169
0.6761	Remote Similarity	NPC473572
0.6761	Remote Similarity	NPC217854
0.6759	Remote Similarity	NPC247146
0.6757	Remote Similarity	NPC168059
0.6757	Remote Similarity	NPC36661
0.6757	Remote Similarity	NPC229442
0.6753	Remote Similarity	NPC109346
0.6739	Remote Similarity	NPC259638
0.6735	Remote Similarity	NPC287780
0.6735	Remote Similarity	NPC472597
0.6735	Remote Similarity	NPC309787
0.6733	Remote Similarity	NPC162659
0.6733	Remote Similarity	NPC248727
0.6733	Remote Similarity	NPC270456
0.6733	Remote Similarity	NPC269091
0.6733	Remote Similarity	NPC265433
0.6733	Remote Similarity	NPC230734
0.6733	Remote Similarity	NPC227503
0.6733	Remote Similarity	NPC302701
0.6733	Remote Similarity	NPC16435
0.6733	Remote Similarity	NPC474639
0.6733	Remote Similarity	NPC306441
0.6728	Remote Similarity	NPC38980
0.6716	Remote Similarity	NPC247871
0.6713	Remote Similarity	NPC5796
0.6713	Remote Similarity	NPC236265
0.6713	Remote Similarity	NPC206487
0.6713	Remote Similarity	NPC25817
0.6711	Remote Similarity	NPC256307
0.6711	Remote Similarity	NPC106215
0.6711	Remote Similarity	NPC66840
0.6708	Remote Similarity	NPC474535
0.669	Remote Similarity	NPC229213
0.669	Remote Similarity	NPC41562
0.6689	Remote Similarity	NPC65530
0.6689	Remote Similarity	NPC326797
0.6689	Remote Similarity	NPC107551
0.6689	Remote Similarity	NPC253105
0.6689	Remote Similarity	NPC35932
0.6689	Remote Similarity	NPC59324
0.6689	Remote Similarity	NPC7903
0.6689	Remote Similarity	NPC160991
0.6689	Remote Similarity	NPC102904
0.6689	Remote Similarity	NPC276490
0.6689	Remote Similarity	NPC211549
0.6689	Remote Similarity	NPC474282
0.6689	Remote Similarity	NPC176051
0.6689	Remote Similarity	NPC184447
0.6689	Remote Similarity	NPC470752
0.6689	Remote Similarity	NPC16208
0.6689	Remote Similarity	NPC201587
0.6689	Remote Similarity	NPC161203
0.6689	Remote Similarity	NPC103976
0.6667	Remote Similarity	NPC203133
0.6667	Remote Similarity	NPC473653
0.6667	Remote Similarity	NPC208950
0.6667	Remote Similarity	NPC17943
0.6667	Remote Similarity	NPC82483
0.6667	Remote Similarity	NPC472093
0.6667	Remote Similarity	NPC234400
0.6667	Remote Similarity	NPC251855
0.6667	Remote Similarity	NPC114325
0.6667	Remote Similarity	NPC474481

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 NPC206183 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	701
0.1-0.2	1649
0.2-0.3	3345
0.3-0.4	2050
0.4-0.5	1119
0.5-0.6	260
0.6-0.7	26
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.7042	Intermediate Similarity	NPD1530	Clinical (unspecified phase)
0.6993	Remote Similarity	NPD1529	Clinical (unspecified phase)
0.6803	Remote Similarity	NPD1612	Clinical (unspecified phase)
0.6803	Remote Similarity	NPD1613	Approved
0.6667	Remote Similarity	NPD9296	Approved
0.6615	Remote Similarity	NPD291	Approved
0.6585	Remote Similarity	NPD9094	Approved
0.6571	Remote Similarity	NPD1548	Phase 1
0.6503	Remote Similarity	NPD1610	Phase 2
0.65	Remote Similarity	NPD1408	Clinical (unspecified phase)
0.6486	Remote Similarity	NPD3027	Phase 3
0.6319	Remote Similarity	NPD915	Approved
0.6309	Remote Similarity	NPD3537	Clinical (unspecified phase)
0.6303	Remote Similarity	NPD4288	Approved
0.6299	Remote Similarity	NPD9365	Approved
0.6224	Remote Similarity	NPD7533	Approved
0.6224	Remote Similarity	NPD7534	Approved
0.62	Remote Similarity	NPD4908	Phase 1
0.619	Remote Similarity	NPD4749	Approved
0.6159	Remote Similarity	NPD4625	Phase 3
0.6159	Remote Similarity	NPD556	Approved
0.6148	Remote Similarity	NPD9093	Approved
0.6144	Remote Similarity	NPD1558	Phase 1
0.6118	Remote Similarity	NPD4907	Clinical (unspecified phase)
0.6098	Remote Similarity	NPD9089	Approved
0.6087	Remote Similarity	NPD1511	Approved
0.6084	Remote Similarity	NPD1934	Approved
0.6081	Remote Similarity	NPD2982	Phase 2
0.6081	Remote Similarity	NPD2983	Phase 2
0.6071	Remote Similarity	NPD228	Approved
0.6058	Remote Similarity	NPD968	Approved
0.6054	Remote Similarity	NPD1091	Approved
0.6054	Remote Similarity	NPD422	Phase 1
0.6037	Remote Similarity	NPD1653	Approved
0.6022	Remote Similarity	NPD4287	Approved
0.6014	Remote Similarity	NPD2981	Phase 2
0.6012	Remote Similarity	NPD1512	Approved
0.5988	Remote Similarity	NPD4010	Discontinued
0.5952	Remote Similarity	NPD1465	Phase 2
0.5952	Remote Similarity	NPD2801	Approved
0.5949	Remote Similarity	NPD3454	Phase 3
0.5921	Remote Similarity	NPD3018	Phase 2
0.5912	Remote Similarity	NPD9244	Approved
0.5909	Remote Similarity	NPD6410	Clinical (unspecified phase)
0.5899	Remote Similarity	NPD290	Approved
0.5899	Remote Similarity	NPD9552	Approved
0.5891	Remote Similarity	NPD9295	Approved
0.5882	Remote Similarity	NPD4868	Clinical (unspecified phase)
0.5867	Remote Similarity	NPD4379	Clinical (unspecified phase)
0.5858	Remote Similarity	NPD2393	Clinical (unspecified phase)
0.5833	Remote Similarity	NPD9299	Approved
0.5818	Remote Similarity	NPD2183	Approved
0.5818	Remote Similarity	NPD2184	Approved
0.5813	Remote Similarity	NPD1552	Clinical (unspecified phase)
0.5813	Remote Similarity	NPD1550	Clinical (unspecified phase)
0.5809	Remote Similarity	NPD1242	Phase 1
0.5797	Remote Similarity	NPD9501	Approved
0.5789	Remote Similarity	NPD3882	Suspended
0.5776	Remote Similarity	NPD1549	Phase 2
0.5767	Remote Similarity	NPD8095	Phase 1
0.5752	Remote Similarity	NPD1469	Clinical (unspecified phase)
0.575	Remote Similarity	NPD6100	Approved
0.575	Remote Similarity	NPD6099	Approved
0.5739	Remote Similarity	NPD6168	Clinical (unspecified phase)
0.5739	Remote Similarity	NPD6166	Phase 2
0.5739	Remote Similarity	NPD6167	Clinical (unspecified phase)
0.5724	Remote Similarity	NPD3225	Approved
0.5714	Remote Similarity	NPD2861	Phase 2
0.5705	Remote Similarity	NPD6859	Clinical (unspecified phase)
0.568	Remote Similarity	NPD4678	Approved
0.568	Remote Similarity	NPD4675	Approved
0.5652	Remote Similarity	NPD1551	Phase 2
0.5644	Remote Similarity	NPD1652	Phase 2
0.5642	Remote Similarity	NPD7054	Approved
0.564	Remote Similarity	NPD2296	Approved
0.5638	Remote Similarity	NPD1797	Approved
0.5638	Remote Similarity	NPD1798	Approved
0.5634	Remote Similarity	NPD2684	Approved
0.5632	Remote Similarity	NPD6234	Discontinued
0.5611	Remote Similarity	NPD7074	Phase 3
0.5611	Remote Similarity	NPD7472	Approved
0.561	Remote Similarity	NPD3750	Approved
0.5608	Remote Similarity	NPD1102	Approved
0.5608	Remote Similarity	NPD1103	Approved
0.5602	Remote Similarity	NPD7212	Phase 2
0.5602	Remote Similarity	NPD4357	Discontinued
0.5602	Remote Similarity	NPD7213	Phase 3
0.56	Remote Similarity	NPD5846	Approved
0.56	Remote Similarity	NPD6516	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