NPASS Compound

Structure

CID7715 OpenBabel06191715332D 44 50 0 0 1 0 0 0 0 0999 V2000 2.3821 4.2830 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4552 0.7397 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3821 -1.7170 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9742 -1.6530 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7880 2.0448 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6463 2.4497 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2094 4.7248 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4894 2.9069 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4142 3.1197 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9449 3.7781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2481 1.7830 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0681 -0.9068 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2481 2.7830 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6605 -0.5174 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4199 1.0695 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1804 3.4075 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0116 4.1757 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3821 0.2830 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1275 -1.0087 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6501 1.2830 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6483 1.7407 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6601 3.8891 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3821 1.2830 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4346 -0.5884 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9772 3.6780 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5161 1.7830 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5161 2.7830 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.9860 0.5088 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0072 3.5338 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6948 4.2362 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5161 -0.2170 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6501 0.2830 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6101 -0.9528 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3936 0.1194 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3997 -0.4768 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7067 -0.0566 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3821 3.2830 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -2.6195 0.1904 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.2763 2.5707 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5946 -0.3696 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5161 -1.2170 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0201 -1.7602 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3826 4.0641 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 1 37 1 0 0 0 0 2 38 1 0 0 0 0 3 41 1 0 0 0 0 4 42 1 0 0 0 0 5 8 1 0 0 0 0 5 21 2 0 0 0 0 6 9 2 0 0 0 0 6 21 1 0 0 0 0 7 10 2 0 0 0 0 7 22 1 0 0 0 0 8 25 2 0 0 0 0 9 25 1 0 0 0 0 10 29 1 0 0 0 0 11 13 1 0 0 0 0 11 23 1 0 0 0 0 12 14 1 0 0 0 0 12 24 1 0 0 0 0 13 37 1 0 0 0 0 14 38 1 0 0 0 0 15 21 1 0 0 0 0 16 22 1 0 0 0 0 17 22 2 0 0 0 0 17 30 1 0 0 0 0 18 23 2 0 0 0 0 18 31 1 0 0 0 0 19 24 2 0 0 0 0 19 33 1 0 0 0 0 20 26 2 0 0 0 0 20 32 1 0 0 0 0 23 26 1 0 0 0 0 24 34 1 0 0 0 0 25 43 1 0 0 0 0 26 27 1 0 0 0 0 27 16 1 1 0 0 0 27 37 1 0 0 0 0 28 15 1 1 0 0 0 28 34 1 0 0 0 0 28 38 1 0 0 0 0 29 30 2 0 0 0 0 29 39 1 0 0 0 0 30 43 1 0 0 0 0 31 32 2 0 0 0 0 31 41 1 0 0 0 0 32 44 1 0 0 0 0 33 35 2 0 0 0 0 33 42 1 0 0 0 0 34 36 2 0 0 0 0 35 36 1 0 0 0 0 35 40 1 0 0 0 0 36 44 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	594.27
Volume:	614.414
LogP:	5.69
LogD:	3.865
LogS:	-4.192
# Rotatable Bonds:	2
TPSA:	83.86
# H-Bond Aceptor:	8
# H-Bond Donor:	2
# Rings:	8
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.27
Synthetic Accessibility Score:	5.759
Fsp3:	0.333
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.653
MDCK Permeability:	2.262005364173092e-05
Pgp-inhibitor:	0.997
Pgp-substrate:	0.43
Human Intestinal Absorption (HIA):	0.006
20% Bioavailability (F20%):	0.691
30% Bioavailability (F30%):	0.986

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.186
Plasma Protein Binding (PPB):	85.11974334716797%
Volume Distribution (VD):	1.009
Pgp-substrate:	15.466694831848145%

ADMET: Metabolism

CYP1A2-inhibitor:	0.081
CYP1A2-substrate:	0.967
CYP2C19-inhibitor:	0.074
CYP2C19-substrate:	0.942
CYP2C9-inhibitor:	0.059
CYP2C9-substrate:	0.51
CYP2D6-inhibitor:	0.015
CYP2D6-substrate:	0.949
CYP3A4-inhibitor:	0.062
CYP3A4-substrate:	0.947

ADMET: Excretion

Clearance (CL):	11.052
Half-life (T1/2):	0.572

ADMET: Toxicity

hERG Blockers:	0.949
Human Hepatotoxicity (H-HT):	0.033
Drug-inuced Liver Injury (DILI):	0.466
AMES Toxicity:	0.173
Rat Oral Acute Toxicity:	0.387
Maximum Recommended Daily Dose:	0.993
Skin Sensitization:	0.925
Carcinogencity:	0.052
Eye Corrosion:	0.003
Eye Irritation:	0.005
Respiratory Toxicity:	0.308

Download Data

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

Natural Product: NPC7715

Natural Product ID:	NPC7715
*Common Name:**	LFFQVHXIFJLJSP-IZLXSDGUSA-N
IUPAC Name:	n.a.
Synonyms:	(+)-Aromoline
Standard InCHIKey:	LFFQVHXIFJLJSP-IZLXSDGUSA-N
Standard InCHI:	InChI=1S/C36H38N2O6/c1-37-13-11-23-18-31(41-3)32-20-26(23)27(37)16-22-7-10-29(39)30(17-22)43-25-8-5-21(6-9-25)15-28-34-24(12-14-38(28)2)19-33(42-4)35(40)36(34)44-32/h5-10,17-20,27-28,39-40H,11-16H2,1-4H3/t27-,28+/m1/s1
SMILES:	COc1cc2CCN([C@H]3c2cc1Oc1c2c(CCN([C@H]2Cc2ccc(Oc4cc(C3)ccc4O)cc2)C)cc(c1O)OC)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL508781
PubChem CID:	362574
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds

*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
NPO5921	Xestospongia caycedoi	Species	Petrosiidae	Eukaryota	n.a.	Fijian	n.a.	PMID[3430171]
NPO17909	Berberis vulgaris	Species	Berberidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30701972]
NPO16121	Pestalotiopsis disseminata	Species	Sporocadaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26641923]
NPO20712	Panax quinquefolius	Species	Araliaceae	Eukaryota	leaves and stems	n.a.	n.a.	PMID[25442304]
NPO10590.1	Morus alba var. multicaulis	Varieties	Moraceae	Eukaryota	Fruits	Zhenjiang, Jiangsu Province, China		PMID[23060696]
NPO8786	Acanthella costata	Species	Melastomataceae	Eukaryota	n.a.	(25 m) at Sykes Reef (Capricorn-Bunker Group Great Barrier Reef), Australia	n.a.	PMID[19243956]
NPO8786	Acanthella costata	Species	Melastomataceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19243956]
NPO16121	Pestalotiopsis disseminata	Species	Sporocadaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16643036]
NPO20891	Coleonema pulchellum	Species	Rutaceae	Eukaryota	n.a.	Costa Rica; Bartica, Guyana	n.a.	PMID[16124770]
NPO14431	Dunaliella salina	Species	Dunaliellaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[14664856]

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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	1
GI50	60
IC50	5
Ki	2
Others	5

Activity Type	# Activity
Cell Line	61
Individual Protein	6
Organism	2
Others	4

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT439	Individual Protein	Butyrylcholinesterase	Homo sapiens	Ki	=	39700.0	nM	PMID[543730]
NPT439	Individual Protein	Butyrylcholinesterase	Homo sapiens	Ki	=	6410.0	nM	PMID[543730]
NPT439	Individual Protein	Butyrylcholinesterase	Homo sapiens	IC50	=	800.0	nM	PMID[543730]
NPT204	Individual Protein	Acetylcholinesterase	Homo sapiens	IC50	>	100000.0	nM	PMID[543730]
NPT1591	Individual Protein	Prolyl endopeptidase	Homo sapiens	IC50	=	189000.0	nM	PMID[543730]
NPT591	Individual Protein	Glycogen synthase kinase-3 beta	Homo sapiens	Inhibition	=	10.0	%	PMID[543730]
NPT2	Others	Unspecified	""	Ratio IC50	=	0.008	n.a.	PMID[543730]
NPT35	Others	n.a.	""	permeability	=	1.8	ucm/s	PMID[543730]
NPT368	Cell Line	SN12C	Homo sapiens	GI50	n.a.	4168.69	nM	PMID[543729]
NPT367	Cell Line	MDA-N	Homo sapiens	GI50	n.a.	10715.19	nM	PMID[543729]

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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 NPC7715 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	365
0.1-0.2	1776
0.2-0.3	8970
0.3-0.4	9442
0.4-0.5	5495
0.5-0.6	8583
0.6-0.7	6506
0.7-0.8	1271
0.8-0.85	138
0.85-0.9	45
0.9-0.95	42
0.95-1	64

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC251735
1.0	High Similarity	NPC104196
1.0	High Similarity	NPC229373
1.0	High Similarity	NPC239824
1.0	High Similarity	NPC15414

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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 NPC7715 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	208
0.1-0.2	792
0.2-0.3	1192
0.3-0.4	2208
0.4-0.5	2416
0.5-0.6	1548
0.6-0.7	643
0.7-0.8	133
0.8-0.85	3
0.85-0.9	1
0.9-0.95	3
0.95-1	3

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
1.0	High Similarity	NPD8054	Approved
1.0	High Similarity	NPD8053	Approved
0.9573	High Similarity	NPD8251	Approved
0.9573	High Similarity	NPD8252	Approved
0.9573	High Similarity	NPD8099	Discontinued

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