NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	159.13
Volume:	172.865
LogP:	-1.179
LogD:	0.057
LogS:	-0.499
# Rotatable Bonds:	5
TPSA:	63.32
# H-Bond Aceptor:	3
# H-Bond Donor:	3
# Rings:	0
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.631
Synthetic Accessibility Score:	2.672
Fsp3:	0.875
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.809
MDCK Permeability:	0.003024076111614704
Pgp-inhibitor:	0.001
Pgp-substrate:	0.008
Human Intestinal Absorption (HIA):	0.009
20% Bioavailability (F20%):	0.003
30% Bioavailability (F30%):	0.001

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.965
Plasma Protein Binding (PPB):	3.313652276992798%
Volume Distribution (VD):	0.654
Pgp-substrate:	86.727783203125%

ADMET: Metabolism

CYP1A2-inhibitor:	0.042
CYP1A2-substrate:	0.078
CYP2C19-inhibitor:	0.02
CYP2C19-substrate:	0.128
CYP2C9-inhibitor:	0.011
CYP2C9-substrate:	0.894
CYP2D6-inhibitor:	0.059
CYP2D6-substrate:	0.269
CYP3A4-inhibitor:	0.016
CYP3A4-substrate:	0.085

ADMET: Excretion

Clearance (CL):	9.111
Half-life (T1/2):	0.775

ADMET: Toxicity

hERG Blockers:	0.022
Human Hepatotoxicity (H-HT):	0.452
Drug-inuced Liver Injury (DILI):	0.028
AMES Toxicity:	0.031
Rat Oral Acute Toxicity:	0.211
Maximum Recommended Daily Dose:	0.386
Skin Sensitization:	0.443
Carcinogencity:	0.277
Eye Corrosion:	0.725
Eye Irritation:	0.489
Respiratory Toxicity:	0.904

Download Data

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

Natural Product: NPC484296

Natural Product ID:	NPC484296
*Common Name:**	AYXYPKUFHZROOJ-ZETCQYMHSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	AYXYPKUFHZROOJ-ZETCQYMHSA-N
Standard InCHI:	InChI=1S/C8H17NO2/c1-6(2)3-7(5-9)4-8(10)11/h6-7H,3-5,9H2,1-2H3,(H,10,11)/t7-/m0/s1
SMILES:	CC(C)C[C@@H](CC(=O)O)CN
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	25271887
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0000265] Carboxylic acids and derivatives [CHEMONTID:0000013] Amino acids, peptides, and analogues [CHEMONTID:0000347] Amino acids and derivatives [CHEMONTID:0001880] Gamma amino acids and derivatives

*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
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	fruit	n.a.	PMID[12802735]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	fruit	n.a.	PMID[18384095]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	leaf	n.a.	PMID[22014120]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	fruit	n.a.	PMID[22014120]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	leaf	n.a.	PMID[22014168]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23540838]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24295708]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	leaf	n.a.	PMID[25102361]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	fruit	n.a.	PMID[25306330]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	Oil	n.a.	n.a.	Database[FooDB]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28608	Olea europaea	Species	Oleaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28608	Olea europaea	Species	Oleaceae	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
ED50	2
IC50	19
Ki	5
Others	35

Activity Type	# Activity
Individual Protein	12
NON-MOLECULAR	1
Organism	14
Others	30
SINGLE PROTEIN	4

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT5837	Individual Protein	Voltage-dependent calcium channel alpha2delta subunit	Sus scrofa	IC50	=	73.0	nM	PMID[16099652]
NPT5837	Individual Protein	Voltage-dependent calcium channel alpha2delta subunit	Sus scrofa	IC50	=	80.0	nM	PMID[19897364]
NPT6603	Individual Protein	P2X purinoceptor 7	Rattus norvegicus	Inhibition	=	31.0	%	PMID[25597334]
NPT612	Individual Protein	Canalicular multispecific organic anion transporter 1	Homo sapiens	IC50	>	133000.0	nM	PMID[23956101]
NPT1249	Individual Protein	Canalicular multispecific organic anion transporter 2	Homo sapiens	IC50	>	133000.0	nM	PMID[23956101]
NPT1028	Individual Protein	Multidrug resistance-associated protein 4	Homo sapiens	IC50	>	133000.0	nM	PMID[23956101]
NPT5836	Individual Protein	Voltage-gated calcium channel alpha2/delta subunit 1	Homo sapiens	Ki	=	19.0	nM	PMID[33591743]
NPT228	Individual Protein	Norepinephrine transporter	Homo sapiens	Ki	>	10000.0	nM	PMID[33591743]
NPT228	Individual Protein	Norepinephrine transporter	Homo sapiens	IC50	>	10000.0	nM	PMID[33591743]
NPT32	Organism	Mus musculus	Mus musculus	ED50	=	20.0	mg.kg-1	DOI[10.1016/S0960-894X(01)80855-6]
NPT2	Others	Unspecified		IC50	=	37.0	nM	DOI[10.1016/S0960-894X(01)80855-6]
NPT2	Others	Unspecified		Inhibition	~	25.0	%	DOI[10.1016/S0960-894X(01)80855-6]
NPT2	Others	Unspecified		Inhibition	~	50.0	%	DOI[10.1016/S0960-894X(01)80855-6]
NPT2	Others	Unspecified		Inhibition	~	75.0	%	DOI[10.1016/S0960-894X(01)80855-6]
NPT2	Others	Unspecified		Inhibition	~	85.0	%	DOI[10.1016/S0960-894X(01)80855-6]
NPT2	Others	Unspecified		Inhibition	~	90.0	%	DOI[10.1016/S0960-894X(01)80855-6]
NPT2	Others	Unspecified		Inhibition	~	94.0	%	DOI[10.1016/S0960-894X(01)80855-6]
NPT2	Others	Unspecified		Inhibition	~	98.0	%	DOI[10.1016/S0960-894X(01)80855-6]
NPT2	Others	Unspecified		Inhibition	~	100.0	%	DOI[10.1016/S0960-894X(01)80855-6]
NPT2	Others	Unspecified		IC50	=	80.0	nM	PMID[15801823]
NPT2	Others	Unspecified		IC50	=	158000.0	nM	PMID[15801823]
NPT2	Others	Unspecified		Ki	=	19.0	nM	PMID[15828841]
NPT2	Others	Unspecified		IC50	=	158000.0	nM	PMID[15828841]
NPT2	Others	Unspecified		IC50	=	284000.0	nM	PMID[16099652]
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	Activity	=	100.0	%	PMID[16099652]
NPT32	Organism	Mus musculus	Mus musculus	Activity	=	100.0	%	PMID[16099652]
NPT32	Organism	Mus musculus	Mus musculus	Activity	=	100.0	%	PMID[16621528]
NPT2	Others	Unspecified		Ki	=	19.0	nM	PMID[16621528]
NPT2	Others	Unspecified		IC50	=	80.0	nM	PMID[19010672]
NPT2	Others	Unspecified		IC50	=	158000.0	nM	PMID[19010672]
NPT32	Organism	Mus musculus	Mus musculus	Activity	=	100.0	%	PMID[19010672]
NPT27	Others	Unspecified		Ratio	=	0.29	n.a.	PMID[19010672]
NPT2	Others	Unspecified		IC50	=	80.0	nM	PMID[19910190]
NPT2	Others	Unspecified		Inhibition	=	92.0	%	PMID[20079559]
NPT2	Others	Unspecified		IC50	=	80.0	nM	PMID[21550803]
NPT2	Others	Unspecified		IC50	=	80.0	nM	PMID[21550802]
NPT2	Others	Unspecified		IC50	=	80.0	nM	PMID[21601457]
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	Activity	=	58.0	%	PMID[23098566]
NPT73	Individual Protein	Solute carrier organic anion transporter family member 1B1	Homo sapiens	Inhibition	=	120.58	%	PMID[23571415]
NPT72	Individual Protein	Solute carrier organic anion transporter family member 1B3	Homo sapiens	Inhibition	=	101.4	%	PMID[23571415]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	Inhibition	=	31.0	%	PMID[24246730]
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	ED50	=	42.2	mg.kg-1	PMID[24948568]
NPT29	Organism	Rattus norvegicus	Rattus norvegicus	Activity	=	5.8	g	PMID[26101568]
NPT2	Others	Unspecified		Activity	=	210.7	pmol/min.mg	PMID[26138193]
NPT2	Others	Unspecified		Activity	=	182.1	pmol/min.mg	PMID[26138193]
NPT713	Individual Protein	Bile salt export pump	Homo sapiens	IC50	>	133000.0	nM	PMID[23956101]
NPT32	Organism	Mus musculus	Mus musculus	Activity	=	98.0	%	PMID[29752183]
NPT2	Others	Unspecified		Activity	=	14.1	%	PMID[27956036]
NPT2	Others	Unspecified		Activity	=	24.34	%	PMID[27956036]
NPT2	Others	Unspecified		Activity	=	15.0	%	PMID[27956036]
NPT2	Others	Unspecified		Activity	=	26.2	%	PMID[27956036]
NPT20555	ORGANISM	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	5.38	%	DOI[10.21203/rs.3.rs-23951/v1]
NPT20556	SINGLE PROTEIN	Replicase polyprotein 1ab	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	12.13	%	DOI[10.6019/CHEMBL4495564]
NPT20555	ORGANISM	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	0.04	%	DOI[10.6019/CHEMBL4495565]
NPT17373	SINGLE PROTEIN	Voltage-gated calcium channel alpha2/delta subunit 2	Homo sapiens	Ki	=	99.0	nM	PMID[33591743]
NPT23196	SINGLE PROTEIN	2-amino-3-carboxymuconate-6-semialdehyde decarboxylase	Homo sapiens	Activity	=	2.98	%	PMID[33369426]
NPT23196	SINGLE PROTEIN	2-amino-3-carboxymuconate-6-semialdehyde decarboxylase	Homo sapiens	Activity	=	97.0	%	PMID[33369426]

☑ 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 NPC484296 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	122
0.1-0.2	12204
0.2-0.3	19854
0.3-0.4	9087
0.4-0.5	1106
0.5-0.6	254
0.6-0.7	50
0.7-0.8	18
0.8-0.85	1
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 NPC484296 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	109
0.1-0.2	3888
0.2-0.3	3641
0.3-0.4	1132
0.4-0.5	245
0.5-0.6	95
0.6-0.7	28
0.7-0.8	8
0.8-0.85	3
0.85-0.9	0
0.9-0.95	0
0.95-1	1

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