NPASS Compound

Structure

NPC486711 OpenBabel06302216032D 22 22 0 0 1 0 0 0 0 0999 V2000 7.7942 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 0.0000 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 1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 2 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 0.0000 -2.0000 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 -2.5981 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -3.0000 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 -3.4641 -3.0000 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 -1.7321 -0.0000 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 0.0000 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 4 1 0 0 0 0 4 5 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 8 9 1 0 0 0 0 10 9 1 6 0 0 0 10 11 1 0 0 0 0 10 21 1 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 12 22 1 0 0 0 0 13 14 1 0 0 0 0 13 19 1 0 0 0 0 14 15 2 0 0 0 0 14 16 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 19 20 2 0 0 0 0 19 21 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	318.26
Volume:	370.25
LogP:	7.533
LogD:	4.749
LogS:	-3.731
# Rotatable Bonds:	13
TPSA:	40.46
# H-Bond Aceptor:	2
# H-Bond Donor:	2
# Rings:	1
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.321
Synthetic Accessibility Score:	2.318
Fsp3:	0.619
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.907
MDCK Permeability:	1.264224738406483e-05
Pgp-inhibitor:	0.002
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.008
20% Bioavailability (F20%):	0.996
30% Bioavailability (F30%):	0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.137
Plasma Protein Binding (PPB):	98.65198516845703%
Volume Distribution (VD):	4.796
Pgp-substrate:	1.0028129816055298%

ADMET: Metabolism

CYP1A2-inhibitor:	0.909
CYP1A2-substrate:	0.187
CYP2C19-inhibitor:	0.85
CYP2C19-substrate:	0.063
CYP2C9-inhibitor:	0.392
CYP2C9-substrate:	0.986
CYP2D6-inhibitor:	0.95
CYP2D6-substrate:	0.473
CYP3A4-inhibitor:	0.666
CYP3A4-substrate:	0.054

ADMET: Excretion

Clearance (CL):	8.112
Half-life (T1/2):	0.634

ADMET: Toxicity

hERG Blockers:	0.158
Human Hepatotoxicity (H-HT):	0.02
Drug-inuced Liver Injury (DILI):	0.014
AMES Toxicity:	0.02
Rat Oral Acute Toxicity:	0.021
Maximum Recommended Daily Dose:	0.526
Skin Sensitization:	0.969
Carcinogencity:	0.037
Eye Corrosion:	0.968
Eye Irritation:	0.952
Respiratory Toxicity:	0.6

Download Data

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

Natural Product: NPC486711

Natural Product ID:	NPC486711
*Common Name:**	XZEIVZDLJSQWCC-CQSZACIVSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	XZEIVZDLJSQWCC-CQSZACIVSA-N
Standard InCHI:	InChI=1S/C18H30O4/c1-3-5-6-7-8-9-10-12-14-13-16(20)17(18(21)22-14)15(19)11-4-2/h14,20H,3-13H2,1-2H3/t14-/m1/s1
SMILES:	CCCCCCCCC[C@@H]1CC(=C(C(=O)CCC)C(=O)O1)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0003909] Fatty Acyls [CHEMONTID:0001722] Fatty alcohol esters

*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
NPO41037	Serratia plymuthica MF371-2	Strain	Yersiniaceae	Bacteria	n.a.	n.a.	n.a.	PMID[29083894]

☑ 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	39
Others	3

Activity Type	# Activity
Cell Line	3
Organism	39

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT65	Cell Line	HepG2	Homo sapiens	CC50	=	33.0	ug.mL-1	PMID[29083894]
NPT1229	Cell Line	Huh-7	Homo sapiens	CC50	=	40.0	ug.mL-1	PMID[29083894]
NPT25	Cell Line	MT4	Homo sapiens	CC50	=	4.7	ug.mL-1	PMID[29083894]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	0.8	ug.mL-1	PMID[29083894]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	0.25	ug.mL-1	PMID[29083894]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	0.4	ug.mL-1	PMID[29083894]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	<=	0.1	ug.mL-1	PMID[29083894]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	0.1	ug.mL-1	PMID[29083894]
NPT18990	ORGANISM	Mycobacterium frederiksbergense	Mycobacterium frederiksbergense	MIC	<=	0.5	ug.mL-1	PMID[29083894]
NPT314	Organism	Bacillus cereus	Bacillus cereus	MIC	<=	1.0	ug.mL-1	PMID[29083894]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	4.0	ug.mL-1	PMID[29083894]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	2.0	ug.mL-1	PMID[29083894]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	1.0	ug.mL-1	PMID[29083894]
NPT17	Organism	Staphylococcus epidermidis	Staphylococcus epidermidis	MIC	=	1.0	ug.mL-1	PMID[29083894]
NPT17	Organism	Staphylococcus epidermidis	Staphylococcus epidermidis	MIC	=	2.0	ug.mL-1	PMID[29083894]
NPT1118	Organism	Streptococcus pneumoniae	Streptococcus pneumoniae	MIC	=	4.0	ug.mL-1	PMID[29083894]
NPT1118	Organism	Streptococcus pneumoniae	Streptococcus pneumoniae	MIC	=	8.0	ug.mL-1	PMID[29083894]
NPT1228	Organism	Streptococcus pyogenes	Streptococcus pyogenes	MIC	=	8.0	ug.mL-1	PMID[29083894]
NPT1531	Organism	Enterococcus faecium	Enterococcus faecium	MIC	=	2.0	ug.mL-1	PMID[29083894]
NPT175	Organism	Enterococcus faecalis	Enterococcus faecalis	MIC	=	2.0	ug.mL-1	PMID[29083894]
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	>	64.0	ug.mL-1	PMID[29083894]
NPT18	Organism	Pseudomonas aeruginosa	Pseudomonas aeruginosa	MIC	>	64.0	ug.mL-1	PMID[29083894]
NPT173	Organism	Klebsiella pneumoniae	Klebsiella pneumoniae	MIC	>	64.0	ug.mL-1	PMID[29083894]
NPT747	Organism	Acinetobacter baumannii	Acinetobacter baumannii	MIC	=	12.0	ug.mL-1	PMID[29083894]

☑ 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 NPC486711 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	196
0.1-0.2	1876
0.2-0.3	6560
0.3-0.4	15964
0.4-0.5	11286
0.5-0.6	4946
0.6-0.7	1727
0.7-0.8	123
0.8-0.85	5
0.85-0.9	2
0.9-0.95	3
0.95-1	9

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 NPC486711 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	216
0.1-0.2	2557
0.2-0.3	3645
0.3-0.4	1966
0.4-0.5	614
0.5-0.6	123
0.6-0.7	27
0.7-0.8	2
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