NPASS Compound

Structure

NPC488196 OpenBabel06302215232D 21 23 0 0 1 0 0 0 0 0999 V2000 2.6272 -1.4706 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1455 -0.5082 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.6474 0.4595 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8822 1.2359 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0582 2.2977 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9074 0.7480 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0701 -0.3299 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3287 -1.1291 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7583 -1.0478 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.3725 -0.1473 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4402 -0.3085 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0514 0.8945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0367 1.2931 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0156 2.3726 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.5209 -0.1606 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0155 -0.5449 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5494 -0.6545 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3464 -0.9525 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1744 -1.4697 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2955 -1.8704 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 6 0 0 0 2 3 1 0 0 0 0 2 7 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 4 6 1 0 0 0 0 6 13 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 15 1 0 0 0 0 9 10 1 0 0 0 0 9 21 1 1 0 0 0 10 11 2 0 0 0 0 10 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 1 0 0 0 13 15 1 0 0 0 0 15 16 1 1 0 0 0 15 17 1 0 0 0 0 17 18 2 0 0 0 0 17 19 1 0 0 0 0 19 20 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	292.13
Volume:	293.028
LogP:	1.68
LogD:	1.296
LogS:	-4.263
# Rotatable Bonds:	2
TPSA:	80.67
# H-Bond Aceptor:	5
# H-Bond Donor:	1
# Rings:	3
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.734
Synthetic Accessibility Score:	5.425
Fsp3:	0.688
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:	-5.062
MDCK Permeability:	2.355549622734543e-05
Pgp-inhibitor:	0.251
Pgp-substrate:	0.002
Human Intestinal Absorption (HIA):	0.019
20% Bioavailability (F20%):	0.12
30% Bioavailability (F30%):	0.568

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.937
Plasma Protein Binding (PPB):	67.59693145751953%
Volume Distribution (VD):	0.517
Pgp-substrate:	38.9544677734375%

ADMET: Metabolism

CYP1A2-inhibitor:	0.018
CYP1A2-substrate:	0.951
CYP2C19-inhibitor:	0.085
CYP2C19-substrate:	0.852
CYP2C9-inhibitor:	0.036
CYP2C9-substrate:	0.053
CYP2D6-inhibitor:	0.002
CYP2D6-substrate:	0.084
CYP3A4-inhibitor:	0.063
CYP3A4-substrate:	0.893

ADMET: Excretion

Clearance (CL):	4.69
Half-life (T1/2):	0.48

ADMET: Toxicity

hERG Blockers:	0.003
Human Hepatotoxicity (H-HT):	0.366
Drug-inuced Liver Injury (DILI):	0.197
AMES Toxicity:	0.154
Rat Oral Acute Toxicity:	0.111
Maximum Recommended Daily Dose:	0.113
Skin Sensitization:	0.067
Carcinogencity:	0.049
Eye Corrosion:	0.046
Eye Irritation:	0.106
Respiratory Toxicity:	0.476

Download Data

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

Natural Product: NPC488196

Natural Product ID:	NPC488196
*Common Name:**	AODYABWPUITGIN-MMYCCSMBSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	AODYABWPUITGIN-MMYCCSMBSA-N
Standard InCHI:	InChI=1S/C16H20O5/c1-8-5-10(17)12-9(8)6-16(20)11(18)7-14(12,2)15(16,3)13(19)21-4/h8,20H,5-7H2,1-4H3/t8-,14+,15-,16-/m0/s1
SMILES:	C[C@H]1CC(=O)C2=C1C[C@@]1(C(=O)C[C@@]2(C)[C@]1(C)C(=O)OC)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic 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

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO1692	Aquilaria malaccensis	Species	Thymelaeaceae	Eukaryota	Seeds	n.a.	n.a.	PMID[28445049]
NPO1692	Aquilaria malaccensis	Species	Thymelaeaceae	Eukaryota	Agarwood	n.a.	n.a.	PMID[29083898]
NPO1692	Aquilaria malaccensis	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30672698]
NPO1692	Aquilaria malaccensis	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7320738]
NPO1692	Aquilaria malaccensis	Species	Thymelaeaceae	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
MIC	10

Activity Type	# Activity
Organism	10

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	430000.0	nM	PMID[29083898]
NPT175	Organism	Enterococcus faecalis	Enterococcus faecalis	MIC	=	430000.0	nM	PMID[29083898]
NPT1531	Organism	Enterococcus faecium	Enterococcus faecium	MIC	=	430000.0	nM	PMID[29083898]
NPT566	Organism	Salmonella typhimurium	Salmonella enterica subsp. enterica serovar Typhimurium	MIC	=	430000.0	nM	PMID[29083898]
NPT173	Organism	Klebsiella pneumoniae	Klebsiella pneumoniae	MIC	=	430000.0	nM	PMID[29083898]
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	=	430000.0	nM	PMID[29083898]
NPT87	Organism	Aspergillus fumigatus	Aspergillus fumigatus	MIC	=	430000.0	nM	PMID[29083898]
NPT329	Organism	Trichophyton rubrum	Trichophyton rubrum	MIC	=	430000.0	nM	PMID[29083898]
NPT330	Organism	Trichophyton mentagrophytes	Trichophyton mentagrophytes	MIC	=	430000.0	nM	PMID[29083898]
NPT20	Organism	Candida albicans	Candida albicans	MIC	=	430000.0	nM	PMID[29083898]

☑ 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 NPC488196 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	237
0.1-0.2	1832
0.2-0.3	8141
0.3-0.4	14092
0.4-0.5	8681
0.5-0.6	6737
0.6-0.7	2687
0.7-0.8	286
0.8-0.85	3
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID

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 NPC488196 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	230
0.1-0.2	2660
0.2-0.3	3902
0.3-0.4	1576
0.4-0.5	428
0.5-0.6	167
0.6-0.7	168
0.7-0.8	19
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

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