NPASS Compound

Structure

NPC474043 OpenBabel07101718192D 31 35 0 0 0 0 0 0 0 0999 V2000 -0.1932 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1369 -5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0029 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5388 -5.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4049 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5388 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2709 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1369 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5878 0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5418 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4049 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5388 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2709 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2709 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5388 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2709 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0029 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4049 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5388 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1369 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4049 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0029 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5878 -0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2788 -1.7601 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.6728 -4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.1369 -4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.1369 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4049 -5.0000 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 5.9540 -0.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.9540 0.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 25 1 0 0 0 0 2 26 1 0 0 0 0 3 27 1 0 0 0 0 4 28 1 0 0 0 0 5 12 2 0 0 0 0 5 14 1 0 0 0 0 6 11 2 0 0 0 0 6 15 1 0 0 0 0 7 11 1 0 0 0 0 7 16 2 0 0 0 0 8 13 2 0 0 0 0 8 17 1 0 0 0 0 9 12 1 0 0 0 0 9 29 1 0 0 0 0 10 30 1 0 0 0 0 10 31 1 0 0 0 0 11 18 1 0 0 0 0 12 19 1 0 0 0 0 13 14 1 0 0 0 0 13 18 1 0 0 0 0 14 20 2 0 0 0 0 15 21 2 0 0 0 0 15 25 1 0 0 0 0 16 21 1 0 0 0 0 16 26 1 0 0 0 0 17 22 2 0 0 0 0 17 30 1 0 0 0 0 18 19 2 0 0 0 0 19 23 1 0 0 0 0 20 22 1 0 0 0 0 20 27 1 0 0 0 0 21 28 1 0 0 0 0 22 31 1 0 0 0 0 23 24 2 0 0 0 0 23 29 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	424.12
Volume:	410.176
LogP:	3.563
LogD:	3.229
LogS:	-6.071
# Rotatable Bonds:	5
TPSA:	81.68
# H-Bond Aceptor:	8
# H-Bond Donor:	0
# Rings:	5
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.57
Synthetic Accessibility Score:	2.763
Fsp3:	0.261
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.956
MDCK Permeability:	6.118580495240167e-05
Pgp-inhibitor:	0.927
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	0.002
30% Bioavailability (F30%):	0.012

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.061
Plasma Protein Binding (PPB):	76.77587127685547%
Volume Distribution (VD):	0.838
Pgp-substrate:	7.967452526092529%

ADMET: Metabolism

CYP1A2-inhibitor:	0.383
CYP1A2-substrate:	0.967
CYP2C19-inhibitor:	0.937
CYP2C19-substrate:	0.787
CYP2C9-inhibitor:	0.527
CYP2C9-substrate:	0.925
CYP2D6-inhibitor:	0.155
CYP2D6-substrate:	0.924
CYP3A4-inhibitor:	0.83
CYP3A4-substrate:	0.375

ADMET: Excretion

Clearance (CL):	9.083
Half-life (T1/2):	0.184

ADMET: Toxicity

hERG Blockers:	0.125
Human Hepatotoxicity (H-HT):	0.132
Drug-inuced Liver Injury (DILI):	0.843
AMES Toxicity:	0.564
Rat Oral Acute Toxicity:	0.04
Maximum Recommended Daily Dose:	0.676
Skin Sensitization:	0.247
Carcinogencity:	0.76
Eye Corrosion:	0.003
Eye Irritation:	0.1
Respiratory Toxicity:	0.498

Download Data

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

Natural Product: NPC474043

Natural Product ID:	NPC474043
*Common Name:**	Dehydro-Beta-Peltatin Methyl Ether
IUPAC Name:	4-methoxy-9-(3,4,5-trimethoxyphenyl)-6H-[2]benzofuro[6,5-f][1,3]benzodioxol-8-one
Synonyms:	Dehydro-Beta-Peltatin Methyl Ether
Standard InCHIKey:	SIJVKLMCZBBMGR-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C23H20O8/c1-25-15-6-11(7-16(26-2)21(15)28-4)18-13-8-17-22(31-10-30-17)20(27-3)14(13)5-12-9-29-23(24)19(12)18/h5-8H,9-10H2,1-4H3
SMILES:	COC1=CC(=CC(=C1OC)OC)C2=C3C(=CC4=C(C5=C(C=C42)OCO5)OC)COC3=O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL459054
PubChem CID:	44584484
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0001610] Arylnaphthalene lignans

*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
NPO17947	Hyptis verticillata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8277312]
NPO17947	Hyptis verticillata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17947	Hyptis verticillata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO17947	Hyptis verticillata	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]

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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
ED50	11
Others	8

Activity Type	# Activity
Cell Line	8
NON-MOLECULAR	10
Organism	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT168	Cell Line	P388	Mus musculus	ED50	=	1.8	ug ml-1	PMID[570213]
NPT762	Cell Line	A-431	Homo sapiens	ED50	>	20.0	ug ml-1	PMID[570213]
NPT1851	Cell Line	Col2	Homo sapiens	ED50	=	3.2	ug ml-1	PMID[570213]
NPT2049	Cell Line	HT	Homo sapiens	ED50	=	3.4	ug ml-1	PMID[570213]
NPT858	Cell Line	LNCaP	Homo sapiens	ED50	=	3.2	ug ml-1	PMID[570213]
NPT1034	Cell Line	Lu1	Homo sapiens	ED50	=	4.3	ug ml-1	PMID[570213]
NPT133	Cell Line	ZR-75-1	Homo sapiens	ED50	>	20.0	ug ml-1	PMID[570213]
NPT91	Cell Line	KB	Homo sapiens	ED50	=	2.2	ug ml-1	PMID[570213]
NPT140	Organism	Artemia	Artemia	LC50	=	434.7	ug.mL-1	PMID[570213]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	ED50	=	2.9	ug ml-1	PMID[570213]

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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 NPC474043 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	439
0.1-0.2	1861
0.2-0.3	3923
0.3-0.4	10127
0.4-0.5	8499
0.5-0.6	3465
0.6-0.7	6666
0.7-0.8	7274
0.8-0.85	351
0.85-0.9	70
0.9-0.95	15
0.95-1	7

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Similarity Score	Similarity Level	Natural Product ID
0.98	High Similarity	NPC234730
0.9615	High Similarity	NPC474042
0.9615	High Similarity	NPC174734
0.9605	High Similarity	NPC115123
0.9605	High Similarity	NPC473900

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 NPC474043 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	382
0.1-0.2	1000
0.2-0.3	1701
0.3-0.4	2761
0.4-0.5	1848
0.5-0.6	939
0.6-0.7	384
0.7-0.8	122
0.8-0.85	11
0.85-0.9	2
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8861	High Similarity	NPD4966	Approved
0.8861	High Similarity	NPD4967	Phase 2
0.8861	High Similarity	NPD4965	Approved
0.875	High Similarity	NPD6234	Discontinued
0.871	High Similarity	NPD6980	Clinical (unspecified phase)

Showing 1 to 5 of 200 entries

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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