NPASS Compound

Structure

CID177281 OpenBabel06191715552D 28 30 0 0 1 0 0 0 0 0999 V2000 -2.5981 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3660 0.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8660 -0.5000 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 3.4641 -2.0000 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 3.4641 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -2.0000 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 -0.8660 -3.5000 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 0.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -3.5000 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 0.8660 -1.5000 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 0.0000 -2.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 3 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 -1.7321 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -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 -1.7321 -2.0000 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 1 11 1 0 0 0 0 2 11 1 0 0 0 0 3 12 1 0 0 0 0 4 21 1 0 0 0 0 5 21 1 0 0 0 0 6 8 2 0 0 0 0 6 13 1 0 0 0 0 7 9 2 0 0 0 0 7 13 1 0 0 0 0 8 14 1 0 0 0 0 9 15 1 0 0 0 0 10 11 1 0 0 0 0 10 16 1 0 0 0 0 12 22 2 0 0 0 0 12 25 1 0 0 0 0 13 18 2 0 0 0 0 14 17 2 0 0 0 0 14 28 1 0 0 0 0 15 23 2 0 0 0 0 15 26 1 0 0 0 0 16 24 2 0 0 0 0 16 27 1 0 0 0 0 17 18 1 0 0 0 0 17 19 1 0 0 0 0 18 26 1 0 0 0 0 19 20 1 0 0 0 0 19 25 1 0 0 0 0 20 21 1 0 0 0 0 20 27 1 0 0 0 0 21 28 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	388.15
Volume:	389.179
LogP:	3.657
LogD:	3.152
LogS:	-3.85
# Rotatable Bonds:	6
TPSA:	92.04
# H-Bond Aceptor:	7
# H-Bond Donor:	0
# Rings:	3
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.584
Synthetic Accessibility Score:	3.571
Fsp3:	0.476
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.716
MDCK Permeability:	3.561761332093738e-05
Pgp-inhibitor:	0.993
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.02
20% Bioavailability (F20%):	0.007
30% Bioavailability (F30%):	0.976

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.175
Plasma Protein Binding (PPB):	86.89579010009766%
Volume Distribution (VD):	0.69
Pgp-substrate:	13.383647918701172%

ADMET: Metabolism

CYP1A2-inhibitor:	0.085
CYP1A2-substrate:	0.102
CYP2C19-inhibitor:	0.535
CYP2C19-substrate:	0.254
CYP2C9-inhibitor:	0.662
CYP2C9-substrate:	0.3
CYP2D6-inhibitor:	0.156
CYP2D6-substrate:	0.091
CYP3A4-inhibitor:	0.463
CYP3A4-substrate:	0.377

ADMET: Excretion

Clearance (CL):	4.235
Half-life (T1/2):	0.642

ADMET: Toxicity

hERG Blockers:	0.006
Human Hepatotoxicity (H-HT):	0.965
Drug-inuced Liver Injury (DILI):	0.954
AMES Toxicity:	0.13
Rat Oral Acute Toxicity:	0.351
Maximum Recommended Daily Dose:	0.027
Skin Sensitization:	0.087
Carcinogencity:	0.904
Eye Corrosion:	0.003
Eye Irritation:	0.013
Respiratory Toxicity:	0.041

Download Data

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

Natural Product: NPC177281

Natural Product ID:	NPC177281
*Common Name:**	(10-Acetyloxy-8,8-Dimethyl-2-Oxo-9,10-Dihydropyrano[2,3-F]Chromen-9-Yl) 3-Methylbutanoate
IUPAC Name:	(10-acetyloxy-8,8-dimethyl-2-oxo-9,10-dihydropyrano[2,3-f]chromen-9-yl) 3-methylbutanoate
Synonyms:
Standard InCHIKey:	ALKTVPFKDYZFGA-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C21H24O7/c1-11(2)10-16(24)27-20-19(25-12(3)22)17-14(28-21(20,4)5)8-6-13-7-9-15(23)26-18(13)17/h6-9,11,19-20H,10H2,1-5H3
SMILES:	CC(C)CC(=O)OC1C(c2c(ccc3ccc(=O)oc23)OC1(C)C)OC(=O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1302867
PubChem CID:	2841560
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000145] Coumarins and derivatives [CHEMONTID:0003484] Pyranocoumarins [CHEMONTID:0003485] Angular pyranocoumarins

*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
NPO7103	Allium sativum	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8350088]
NPO7103	Allium sativum	Species	Amaryllidaceae	Eukaryota	garlic skin	n.a.	n.a.	PMID[25726329]
NPO7103	Allium sativum	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25650289]
NPO7103	Allium sativum	Species	Amaryllidaceae	Eukaryota	n.a.	bulb	n.a.	PMID[24508058]
NPO7103	Allium sativum	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23865201]
NPO7103	Allium sativum	Species	Amaryllidaceae	Eukaryota	Essential oil	n.a.	n.a.	PMID[23163425]
NPO7103	Allium sativum	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18460139]
NPO7103	Allium sativum	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18326559]
NPO7103	Allium sativum	Species	Amaryllidaceae	Eukaryota	n.a.	leaf	n.a.	PMID[17262437]
NPO7103	Allium sativum	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.3923/pjbs.2013.1138.1144]

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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
Potency	37

Activity Type	# Activity
Individual Protein	33
Organism	1
Others	3

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT50	Individual Protein	Tyrosyl-DNA phosphodiesterase 1	Homo sapiens	Potency	n.a.	8199.5	nM	PMID[506623]
NPT50	Individual Protein	Tyrosyl-DNA phosphodiesterase 1	Homo sapiens	Potency	n.a.	20596.2	nM	PMID[506623]
NPT2	Others	Unspecified		Potency	n.a.	11220.2	nM	PMID[506623]
NPT2	Others	Unspecified		Potency	n.a.	35481.3	nM	PMID[506623]
NPT149	Individual Protein	Endoplasmic reticulum-associated amyloid beta-peptide-binding protein	Homo sapiens	Potency	=	25118.9	nM	PMID[506622]
NPT48	Individual Protein	Lysine-specific demethylase 4D-like	Homo sapiens	Potency	=	25118.9	nM	PMID[506622]
NPT531	Individual Protein	Nuclear receptor ROR-gamma	Mus musculus	Potency	=	2818.4	nM	PMID[506622]
NPT151	Individual Protein	15-hydroxyprostaglandin dehydrogenase [NAD+]	Homo sapiens	Potency	=	28183.8	nM	PMID[506622]
NPT109	Individual Protein	Cytochrome P450 3A4	Homo sapiens	Potency	=	19952.6	nM	PMID[506622]
NPT61	Individual Protein	Beta-glucocerebrosidase	Homo sapiens	Potency	n.a.	28183.8	nM	PMID[506622]

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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 NPC177281 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	416
0.1-0.2	1646
0.2-0.3	4074
0.3-0.4	9180
0.4-0.5	9424
0.5-0.6	4062
0.6-0.7	5920
0.7-0.8	5532
0.8-0.85	1848
0.85-0.9	392
0.9-0.95	154
0.95-1	49

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC55615
1.0	High Similarity	NPC149320
1.0	High Similarity	NPC160727
1.0	High Similarity	NPC476455
1.0	High Similarity	NPC128529

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 NPC177281 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	360
0.1-0.2	951
0.2-0.3	1755
0.3-0.4	2640
0.4-0.5	1889
0.5-0.6	1034
0.6-0.7	361
0.7-0.8	116
0.8-0.85	34
0.85-0.9	8
0.9-0.95	2
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.875	High Similarity	NPD5123	Clinical (unspecified phase)
0.875	High Similarity	NPD5124	Phase 1
0.8322	Intermediate Similarity	NPD1652	Phase 2
0.8212	Intermediate Similarity	NPD7096	Clinical (unspecified phase)
0.8134	Intermediate Similarity	NPD422	Phase 1

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