NPASS Compound

Structure

NPC469153 OpenBabel06302215352D 32 35 0 0 1 0 0 0 0 0999 V2000 5.8551 -1.2929 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5622 -2.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 7.4282 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.2942 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.1603 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.1603 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.2942 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.4282 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5622 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5622 -5.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.6962 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8301 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9641 -3.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 3.9641 -2.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 4.8301 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6962 -2.5000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 3.0981 -2.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 2.2321 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2321 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0981 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0981 -5.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3660 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5000 -3.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.3660 -5.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3660 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0981 -1.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 3.9641 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2321 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9641 -4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.8301 -5.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.2942 -5.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.4861 -1.6173 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 16 1 0 0 0 0 2 3 1 0 0 0 0 2 32 1 0 0 0 0 3 8 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 7 31 1 0 0 0 0 8 9 1 0 0 0 0 9 10 2 0 0 0 0 9 11 1 0 0 0 0 11 16 1 0 0 0 0 11 12 2 0 0 0 0 12 13 1 0 0 0 0 12 30 1 0 0 0 0 13 20 1 0 0 0 0 13 14 1 0 0 0 0 13 29 1 0 0 0 0 14 15 1 0 0 0 0 14 17 1 0 0 0 0 15 16 1 0 0 0 0 17 18 1 0 0 0 0 17 26 1 0 0 0 0 18 19 2 0 0 0 0 18 25 1 0 0 0 0 19 20 1 0 0 0 0 19 22 1 0 0 0 0 20 21 2 0 0 0 0 22 23 2 0 0 0 0 22 24 1 0 0 0 0 26 27 1 0 0 0 0 26 28 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	444.15
Volume:	426.066
LogP:	0.477
LogD:	-0.156
LogS:	-1.692
# Rotatable Bonds:	2
TPSA:	175.3
# H-Bond Aceptor:	10
# H-Bond Donor:	5
# Rings:	4
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.397
Synthetic Accessibility Score:	4.593
Fsp3:	0.5
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.302
MDCK Permeability:	0.00011751354031730443
Pgp-inhibitor:	0.008
Pgp-substrate:	0.999
Human Intestinal Absorption (HIA):	0.015
20% Bioavailability (F20%):	0.001
30% Bioavailability (F30%):	0.001

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.029
Plasma Protein Binding (PPB):	40.291481018066406%
Volume Distribution (VD):	1.062
Pgp-substrate:	59.41261672973633%

ADMET: Metabolism

CYP1A2-inhibitor:	0.012
CYP1A2-substrate:	0.141
CYP2C19-inhibitor:	0.017
CYP2C19-substrate:	0.062
CYP2C9-inhibitor:	0.009
CYP2C9-substrate:	0.058
CYP2D6-inhibitor:	0.008
CYP2D6-substrate:	0.111
CYP3A4-inhibitor:	0.086
CYP3A4-substrate:	0.552

ADMET: Excretion

Clearance (CL):	3.443
Half-life (T1/2):	0.029

ADMET: Toxicity

hERG Blockers:	0.032
Human Hepatotoxicity (H-HT):	0.077
Drug-inuced Liver Injury (DILI):	0.871
AMES Toxicity:	0.012
Rat Oral Acute Toxicity:	0.949
Maximum Recommended Daily Dose:	0.016
Skin Sensitization:	0.181
Carcinogencity:	0.425
Eye Corrosion:	0.006
Eye Irritation:	0.014
Respiratory Toxicity:	0.972

Download Data

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

Natural Product: NPC469153

Natural Product ID:	NPC469153
*Common Name:**	XMEVHPAGJVLHIG-FMZCEJRJSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	XMEVHPAGJVLHIG-FMZCEJRJSA-N
Standard InCHI:	InChI=1S/C22H24N2O8.ClH/c1-21(31)8-5-4-6-11(25)12(8)16(26)13-9(21)7-10-15(24(2)3)17(27)14(20(23)30)19(29)22(10,32)18(13)28;/h4-6,9-10,15,25,27-28,31-32H,7H2,1-3H3,(H2,23,30);1H/t9-,10-,15-,21+,22-;/m0./s1
SMILES:	C[C@]1(c2cccc(c2C(=O)C2=C([C@]3([C@@H](C[C@H]12)[C@@H](C(=C(C3=O)C(=N)O)O)N(C)C)O)O)O)O.Cl
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000181] Tetracyclines

*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
NPO18453	Helichrysum odoratissimum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[2778452]
NPO18453	Helichrysum odoratissimum	Species	Asteraceae	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	67
Others	14

Activity Type	# Activity
Individual Protein	2
NON-MOLECULAR	29
Organism	49
SINGLE PROTEIN	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	MIC	=	3.9	ug.mL-1	PMID[17060530]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	MIC	=	31.2	ug.mL-1	PMID[17060530]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	MIC	=	15.6	ug.mL-1	PMID[17060530]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	MIC	=	125.0	ug.mL-1	PMID[17060530]
NPT2900	Organism	Bifidobacterium longum	Bifidobacterium longum	MIC	=	62.5	ug.mL-1	PMID[17060530]
NPT2900	Organism	Bifidobacterium longum	Bifidobacterium longum	MIC	=	31.2	ug.mL-1	PMID[17060530]
NPT2900	Organism	Bifidobacterium longum	Bifidobacterium longum	MIC	=	15.6	ug.mL-1	PMID[17060530]
NPT2901	Organism	Bifidobacterium thermophilum	Bifidobacterium thermophilum	MIC	=	62.5	ug.mL-1	PMID[17060530]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	MIC	=	62.5	ug.mL-1	PMID[17060530]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	MIC	=	0.98	ug.mL-1	PMID[17060530]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	MIC	=	250.0	ug.mL-1	PMID[17060530]
NPT2900	Organism	Bifidobacterium longum	Bifidobacterium longum	MIC	=	0.98	ug.mL-1	PMID[17060530]
NPT2901	Organism	Bifidobacterium thermophilum	Bifidobacterium thermophilum	MIC	=	125.0	ug.mL-1	PMID[17060530]
NPT2900	Organism	Bifidobacterium longum	Bifidobacterium longum	MIC	=	125.0	ug.mL-1	PMID[17060530]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	MIC	=	7.8	ug.mL-1	PMID[17060530]
NPT2900	Organism	Bifidobacterium longum	Bifidobacterium longum	MIC	=	7.8	ug.mL-1	PMID[17060530]
NPT2901	Organism	Bifidobacterium thermophilum	Bifidobacterium thermophilum	MIC	=	15.6	ug.mL-1	PMID[17060530]
NPT1033	Organism	Enterobacter cloacae	Enterobacter cloacae	MIC	=	12.5	ug.mL-1	PMID[2778452]
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	=	6.25	ug.mL-1	PMID[2778452]
NPT173	Organism	Klebsiella pneumoniae	Klebsiella pneumoniae	MIC	=	12.5	ug.mL-1	PMID[2778452]
NPT766	Organism	Proteus vulgaris	Proteus vulgaris	MIC	=	25.0	ug.mL-1	PMID[2778452]
NPT18	Organism	Pseudomonas aeruginosa	Pseudomonas aeruginosa	MIC	=	100.0	ug.mL-1	PMID[2778452]
NPT331	Organism	Ralstonia solanacearum	Ralstonia solanacearum	MIC	=	100.0	ug.mL-1	PMID[2778452]
NPT566	Organism	Salmonella typhimurium	Salmonella enterica subsp. enterica serovar Typhimurium	MIC	=	12.5	ug.mL-1	PMID[2778452]
NPT1248	Organism	Serratia marcescens	Serratia marcescens	MIC	=	25.0	ug.mL-1	PMID[2778452]
NPT3152	Organism	Shigella dysenteriae	Shigella dysenteriae	MIC	=	0.78	ug.mL-1	PMID[2778452]
NPT79	Organism	Bacillus subtilis	Bacillus subtilis	MIC	=	3.12	ug.mL-1	PMID[2778452]
NPT602	Organism	Mycobacterium smegmatis	Mycobacterium smegmatis	MIC	=	100.0	ug.mL-1	PMID[2778452]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	100.0	ug.mL-1	PMID[2778452]
NPT1228	Organism	Streptococcus pyogenes	Streptococcus pyogenes	MIC	=	6.25	ug.mL-1	PMID[2778452]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	IZ	=	28.0	mm	PMID[18234501]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	IZ	=	29.0	mm	PMID[18234501]
NPT729	Organism	Micrococcus luteus	Micrococcus luteus	MIC	=	0.1	ug.mL-1	PMID[21388191]
NPT79	Organism	Bacillus subtilis	Bacillus subtilis	MIC	=	0.05	ug.mL-1	PMID[21388191]
NPT314	Organism	Bacillus cereus	Bacillus cereus	MIC	=	1.5	ug.mL-1	PMID[21388191]
NPT175	Organism	Enterococcus faecalis	Enterococcus faecalis	MIC	=	0.2	ug.mL-1	PMID[21388191]
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	=	0.8	ug.mL-1	PMID[21388191]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	0.05	ug.mL-1	PMID[21388191]
NPT1286	Organism	Pectobacterium carotovorum	Pectobacterium carotovorum	IZ	=	34.67	mm	PMID[17628075]
NPT19	Organism	Escherichia coli	Escherichia coli	IZ	=	24.0	mm	PMID[17628075]
NPT1242	Organism	Salmonella typhi	Salmonella enterica subsp. enterica serovar Typhi	IZ	=	18.67	mm	PMID[17628075]
NPT175	Organism	Enterococcus faecalis	Enterococcus faecalis	IZ	=	31.67	mm	PMID[17628075]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	IZ	=	16.67	mm	PMID[17628075]
NPT314	Organism	Bacillus cereus	Bacillus cereus	IZ	=	18.33	mm	PMID[17628075]
NPT72	Individual Protein	Solute carrier organic anion transporter family member 1B3	Homo sapiens	Inhibition	=	97.72	%	PMID[23571415]
NPT73	Individual Protein	Solute carrier organic anion transporter family member 1B1	Homo sapiens	Inhibition	=	118.05	%	PMID[23571415]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	MIC	=	1.0	ug.mL-1	PMID[25293447]
NPT20555	ORGANISM	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	2.3	%	DOI[10.21203/rs.3.rs-23951/v1]
NPT20556	SINGLE PROTEIN	Replicase polyprotein 1ab	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	30.99	%	DOI[10.6019/CHEMBL4495564]
NPT20555	ORGANISM	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	0.46	%	DOI[10.6019/CHEMBL4495565]

☑ 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 NPC469153 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	267
0.1-0.2	1151
0.2-0.3	4221
0.3-0.4	11577
0.4-0.5	8000
0.5-0.6	14142
0.6-0.7	3281
0.7-0.8	46
0.8-0.85	2
0.85-0.9	4
0.9-0.95	2
0.95-1	4

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 NPC469153 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	168
0.1-0.2	542
0.2-0.3	1027
0.3-0.4	2124
0.4-0.5	3039
0.5-0.6	1855
0.6-0.7	352
0.7-0.8	17
0.8-0.85	4
0.85-0.9	6
0.9-0.95	10
0.95-1	6

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