NPASS Compound

Structure

NPC482443 OpenBabel06302215362D 26 27 0 0 1 0 0 0 0 0999 V2000 2.1713 2.4316 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1767 2.3271 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7700 1.4135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3578 0.6045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9511 -0.3090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.8171 0.1910 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6831 -0.3090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.6831 -1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1831 -2.1750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6831 -1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8171 -1.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9511 -1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.6180 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3090 -2.5691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2872 -2.7770 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3601 -3.3122 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5878 -0.8090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3090 0.9511 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4538 -0.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4538 0.6910 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.3198 -0.8090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.1859 -0.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4538 -1.3090 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.5491 0.1910 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5890 3.1361 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 26 1 0 0 0 0 3 4 1 0 0 0 0 5 4 1 1 0 0 0 5 12 1 0 0 0 0 5 18 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 7 25 1 1 0 0 0 8 9 1 0 0 0 0 8 10 1 0 0 0 0 8 11 1 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 13 14 1 0 0 0 0 13 17 1 0 0 0 0 14 15 2 0 0 0 0 14 16 1 0 0 0 0 17 18 1 0 0 0 0 17 20 1 0 0 0 0 17 24 1 1 0 0 0 18 19 2 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 22 23 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	366.17
Volume:	368.417
LogP:	2.054
LogD:	1.628
LogS:	-3.301
# Rotatable Bonds:	5
TPSA:	110.13
# H-Bond Aceptor:	7
# H-Bond Donor:	2
# Rings:	2
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.437
Synthetic Accessibility Score:	4.59
Fsp3:	0.632
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:	-5.097
MDCK Permeability:	2.4064389435807243e-05
Pgp-inhibitor:	0.772
Pgp-substrate:	0.969
Human Intestinal Absorption (HIA):	0.065
20% Bioavailability (F20%):	0.106
30% Bioavailability (F30%):	0.678

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.479
Plasma Protein Binding (PPB):	80.9089584350586%
Volume Distribution (VD):	2.213
Pgp-substrate:	16.32170295715332%

ADMET: Metabolism

CYP1A2-inhibitor:	0.009
CYP1A2-substrate:	0.21
CYP2C19-inhibitor:	0.135
CYP2C19-substrate:	0.848
CYP2C9-inhibitor:	0.02
CYP2C9-substrate:	0.03
CYP2D6-inhibitor:	0.001
CYP2D6-substrate:	0.055
CYP3A4-inhibitor:	0.076
CYP3A4-substrate:	0.93

ADMET: Excretion

Clearance (CL):	2.446
Half-life (T1/2):	0.255

ADMET: Toxicity

hERG Blockers:	0.007
Human Hepatotoxicity (H-HT):	0.911
Drug-inuced Liver Injury (DILI):	0.935
AMES Toxicity:	0.699
Rat Oral Acute Toxicity:	0.11
Maximum Recommended Daily Dose:	0.037
Skin Sensitization:	0.102
Carcinogencity:	0.049
Eye Corrosion:	0.229
Eye Irritation:	0.131
Respiratory Toxicity:	0.1

Download Data

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

Natural Product: NPC482443

Natural Product ID:	NPC482443
*Common Name:**	ZQRQLDLOXZSDNY-QQGDVQBRSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	ZQRQLDLOXZSDNY-QQGDVQBRSA-N
Standard InCHI:	InChI=1S/C19H26O7/c1-10(2)7-8-18-9-12(21)17(4,5)26-14(18)13(11(3)20)19(24,15(18)22)16(23)25-6/h7,12,21,24H,8-9H2,1-6H3/t12-,18-,19-/m1/s1
SMILES:	CC(=CC[C@@]12C[C@H](C(C)(C)OC1=C(C(=O)C)[C@@](C2=O)(C(=O)OC)O)O)C
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
NPO5601	Evodia lepta	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[29847131]
NPO5601	Evodia lepta	Species	Rutaceae	Eukaryota	Leaves	n.a.	n.a.	PMID[31393125]
NPO5601	Evodia lepta	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5601	Evodia lepta	Species	Rutaceae	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	13
Others	2

Activity Type	# Activity
Cell Line	2
Organism	13

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT737	Cell Line	HUVEC	Homo sapiens	Activity	=	102.6	%	PMID[30998015]
NPT737	Cell Line	HUVEC	Homo sapiens	Activity	=	103.9	%	PMID[30998015]
NPT20	Organism	Candida albicans	Candida albicans	MIC	=	136600.0	nM	PMID[29847131]
NPT187	Organism	Issatchenkia orientalis	Pichia kudriavzevii	MIC	=	136600.0	nM	PMID[29847131]
NPT2578	Organism	Pichia guilliermondii	Meyerozyma guilliermondii	MIC	=	68300.0	nM	PMID[29847131]
NPT820	Organism	Clavispora lusitaniae	Clavispora lusitaniae	MIC	=	68300.0	nM	PMID[29847131]
NPT554	Organism	Candida glabrata	Candida glabrata	MIC	=	34200.0	nM	PMID[29847131]
NPT188	Organism	Candida parapsilosis	Candida parapsilosis	MIC	=	17100.0	nM	PMID[29847131]
NPT1033	Organism	Enterobacter cloacae	Enterobacter cloacae	MIC	>	200000.0	nM	PMID[29847131]
NPT173	Organism	Klebsiella pneumoniae	Klebsiella pneumoniae	MIC	>	200000.0	nM	PMID[29847131]
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	>	200000.0	nM	PMID[29847131]
NPT175	Organism	Enterococcus faecalis	Enterococcus faecalis	MIC	>	200000.0	nM	PMID[29847131]
NPT79	Organism	Bacillus subtilis	Bacillus subtilis	MIC	>	200000.0	nM	PMID[29847131]
NPT17	Organism	Staphylococcus epidermidis	Staphylococcus epidermidis	MIC	>	200000.0	nM	PMID[29847131]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	>	200000.0	nM	PMID[29847131]

☑ 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 NPC482443 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	205
0.1-0.2	1269
0.2-0.3	4242
0.3-0.4	7812
0.4-0.5	13868
0.5-0.6	9153
0.6-0.7	5086
0.7-0.8	1035
0.8-0.85	23
0.85-0.9	1
0.9-0.95	0
0.95-1	3

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 NPC482443 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	179
0.1-0.2	1682
0.2-0.3	3596
0.3-0.4	2346
0.4-0.5	899
0.5-0.6	308
0.6-0.7	134
0.7-0.8	6
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