NPASS Compound

Structure

CID110677 OpenBabel06191715462D 54 61 0 0 0 0 0 0 0 0999 V2000 -12.9904 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.2583 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.1244 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.1244 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.9904 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.2583 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.5263 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.5263 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.1244 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -13.8564 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.3923 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.3923 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 12 2 0 0 0 0 1 13 1 0 0 0 0 2 12 1 0 0 0 0 2 15 2 0 0 0 0 3 13 2 0 0 0 0 3 15 1 0 0 0 0 4 14 2 0 0 0 0 4 18 1 0 0 0 0 5 14 1 0 0 0 0 5 26 2 0 0 0 0 6 16 2 0 0 0 0 6 19 1 0 0 0 0 7 16 1 0 0 0 0 7 20 2 0 0 0 0 8 17 2 0 0 0 0 8 21 1 0 0 0 0 9 17 1 0 0 0 0 9 27 2 0 0 0 0 10 22 2 0 0 0 0 10 25 1 0 0 0 0 11 23 2 0 0 0 0 11 24 1 0 0 0 0 12 37 1 0 0 0 0 13 38 1 0 0 0 0 14 39 1 0 0 0 0 15 49 1 0 0 0 0 16 50 1 0 0 0 0 17 48 1 0 0 0 0 18 29 2 0 0 0 0 18 40 1 0 0 0 0 19 28 2 0 0 0 0 19 41 1 0 0 0 0 20 28 1 0 0 0 0 20 42 1 0 0 0 0 21 30 2 0 0 0 0 21 43 1 0 0 0 0 22 31 1 0 0 0 0 22 44 1 0 0 0 0 23 32 1 0 0 0 0 23 45 1 0 0 0 0 24 33 2 0 0 0 0 24 46 1 0 0 0 0 25 34 2 0 0 0 0 25 47 1 0 0 0 0 26 29 1 0 0 0 0 26 51 1 0 0 0 0 27 30 1 0 0 0 0 27 52 1 0 0 0 0 28 48 1 0 0 0 0 29 53 1 0 0 0 0 30 54 1 0 0 0 0 31 35 2 0 0 0 0 31 49 1 0 0 0 0 32 36 2 0 0 0 0 32 50 1 0 0 0 0 33 36 1 0 0 0 0 33 51 1 0 0 0 0 34 35 1 0 0 0 0 34 52 1 0 0 0 0 35 54 1 0 0 0 0 36 53 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	742.08
Volume:	673.528
LogP:	5.871
LogD:	2.557
LogS:	-11.227
# Rotatable Bonds:	6
TPSA:	287.14
# H-Bond Aceptor:	18
# H-Bond Donor:	11
# Rings:	8
# Heavy Atoms:	18

MedChem Properties

QED Drug-Likeness Score:	0.078
Synthetic Accessibility Score:	3.775
Fsp3:	0.0
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.841
MDCK Permeability:	1.0289424608345143e-05
Pgp-inhibitor:	0.21
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.799
20% Bioavailability (F20%):	0.317
30% Bioavailability (F30%):	0.967

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.002
Plasma Protein Binding (PPB):	91.4821548461914%
Volume Distribution (VD):	0.06
Pgp-substrate:	13.420221328735352%

ADMET: Metabolism

CYP1A2-inhibitor:	0.684
CYP1A2-substrate:	0.081
CYP2C19-inhibitor:	0.063
CYP2C19-substrate:	0.026
CYP2C9-inhibitor:	0.291
CYP2C9-substrate:	0.433
CYP2D6-inhibitor:	0.0
CYP2D6-substrate:	0.217
CYP3A4-inhibitor:	0.038
CYP3A4-substrate:	0.072

ADMET: Excretion

Clearance (CL):	7.761
Half-life (T1/2):	0.698

ADMET: Toxicity

hERG Blockers:	0.042
Human Hepatotoxicity (H-HT):	0.005
Drug-inuced Liver Injury (DILI):	0.729
AMES Toxicity:	0.084
Rat Oral Acute Toxicity:	1.0
Maximum Recommended Daily Dose:	0.998
Skin Sensitization:	0.994
Carcinogencity:	0.074
Eye Corrosion:	0.003
Eye Irritation:	0.964
Respiratory Toxicity:	0.073

Download Data

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

Natural Product: NPC110677

Natural Product ID:	NPC110677
*Common Name:**	Dieckol
IUPAC Name:	4-[4-[6-(3,5-dihydroxyphenoxy)-4,7,9-trihydroxydibenzo-p-dioxin-2-yl]oxy-3,5-dihydroxyphenoxy]dibenzo-p-dioxin-1,3,6,8-tetrol
Synonyms:	Dieckol
Standard InCHIKey:	DRZQFGYIIYNNEC-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C36H22O18/c37-12-1-13(38)3-15(2-12)49-31-22(44)10-25(47)34-35(31)54-30-21(43)8-17(9-27(30)52-34)48-28-19(41)6-16(7-20(28)42)50-32-23(45)11-24(46)33-36(32)53-29-18(40)4-14(39)5-26(29)51-33/h1-11,37-47H
SMILES:	Oc1cc(O)cc(c1)Oc1c(O)cc(c2c1Oc1c(O)cc(cc1O2)Oc1c(O)cc(cc1O)Oc1c(O)cc(c2c1Oc1c(O)cc(cc1O2)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL508791
PubChem CID:	3008868
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000238] Tannins

*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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO22789	Ecklonia cava	Species	Lessoniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23647823]
NPO27567	Eisenia bicyclis	Species	Lessoniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20462757]
NPO22789	Ecklonia cava	Species	Lessoniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19201199]
NPO22789	Ecklonia cava	Species	Lessoniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18693022]
NPO27567	Eisenia bicyclis	Species	Lessoniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[14738398]
NPO27567	Eisenia bicyclis	Species	Lessoniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[14575430]
NPO14337	Ecklonia stolonifera	Species	Lessoniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12913249]
NPO22789	Ecklonia cava	Species	Lessoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14337	Ecklonia stolonifera	Species	Lessoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27567	Eisenia bicyclis	Species	Lessoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

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☑ 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

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Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
No data available in table

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☑ 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
IC50	9
Kd	1
Ki	2
Others	17

Activity Type	# Activity
Cell Line	7
Individual Protein	13
NON-MOLECULAR	3
Organism	1
Others	5

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT2	Others	Unspecified		IC50	=	2700.0	nM	PMID[550268]
NPT189	Cell Line	Vero	Chlorocebus aethiops	CC50	>	200000.0	nM	PMID[550267]
NPT1595	Individual Protein	Replicase polyprotein 1ab	SARS coronavirus	IC50	=	68100.0	nM	PMID[550267]
NPT1595	Individual Protein	Replicase polyprotein 1ab	SARS coronavirus	Ratio IC50	=	60.0	n.a.	PMID[550267]
NPT1595	Individual Protein	Replicase polyprotein 1ab	SARS coronavirus	Ratio IC50	=	50.0	n.a.	PMID[550267]
NPT1595	Individual Protein	Replicase polyprotein 1ab	SARS coronavirus	Ratio IC50	=	30.0	n.a.	PMID[550267]
NPT1595	Individual Protein	Replicase polyprotein 1ab	SARS coronavirus	Kd	=	10300.0	nM	PMID[550267]
NPT1595	Individual Protein	Replicase polyprotein 1ab	SARS coronavirus	IC50	=	2700.0	nM	PMID[550267]
NPT1595	Individual Protein	Replicase polyprotein 1ab	SARS coronavirus	Ki	=	2400.0	nM	PMID[550267]
NPT2	Others	Unspecified		Ratio CC50/IC50	>	2.9	n.a.	PMID[550267]

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☑ 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 NPC110677 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	797
0.1-0.2	4304
0.2-0.3	13661
0.3-0.4	6031
0.4-0.5	5473
0.5-0.6	7344
0.6-0.7	4440
0.7-0.8	630
0.8-0.85	8
0.85-0.9	2
0.9-0.95	2
0.95-1	5

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Similarity Score	Similarity Level	Natural Product ID
0.9664	High Similarity	NPC105147
0.9664	High Similarity	NPC126216
0.9664	High Similarity	NPC228875
0.9496	High Similarity	NPC205850
0.9328	High Similarity	NPC214289

Showing 1 to 5 of 200 entries

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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 NPC110677 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	582
0.1-0.2	1251
0.2-0.3	3195
0.3-0.4	2264
0.4-0.5	1197
0.5-0.6	569
0.6-0.7	86
0.7-0.8	6
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.7574	Intermediate Similarity	NPD1530	Clinical (unspecified phase)
0.7518	Intermediate Similarity	NPD1529	Clinical (unspecified phase)
0.7305	Intermediate Similarity	NPD1612	Clinical (unspecified phase)
0.7305	Intermediate Similarity	NPD1613	Approved
0.7214	Intermediate Similarity	NPD3027	Phase 3

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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