NPASS Compound

Structure

NPC483358 OpenBabel06302215502D 28 31 0 0 1 0 0 0 0 0999 V2000 4.8359 -6.5019 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7269 -6.0480 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8834 -5.0603 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8710 -4.9038 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.3250 -4.0128 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7804 -3.1742 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2344 -2.2831 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.2330 -2.2308 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.7777 -3.0695 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.3237 -3.9605 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.3250 -5.7948 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 6.6179 -6.5019 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1763 -4.3532 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2103 -4.6120 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 3.5032 -3.9049 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 2.5032 -3.9049 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7961 -4.6120 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5032 -2.9049 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2.1942 -1.9538 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.2431 -1.6448 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0352 -0.6666 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5000 -2.3139 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0032 -1.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5032 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5032 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8122 -1.9538 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 3.5032 -2.9049 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 5.4351 -3.3872 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 12 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 3 13 1 0 0 0 0 4 5 1 0 0 0 0 4 11 2 0 0 0 0 5 10 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 8 9 2 0 0 0 0 9 10 1 0 0 0 0 11 12 1 0 0 0 0 13 14 2 0 0 0 0 13 28 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 15 27 1 0 0 0 0 16 17 2 0 0 0 0 16 18 1 0 0 0 0 18 27 1 0 0 0 0 18 19 1 0 0 0 0 19 20 1 0 0 0 0 19 23 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 23 24 1 0 0 0 0 23 25 1 0 0 0 0 23 26 1 0 0 0 0 26 27 1 0 0 0 0 M CHG 1 28 -1 M END $$$$

Physi-Chem Properties

Molecular Weight:	318.22
Volume:	347.268
LogP:	2.526
LogD:	2.354
LogS:	-4.47
# Rotatable Bonds:	1
TPSA:	57.53
# H-Bond Aceptor:	3
# H-Bond Donor:	2
# Rings:	3
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.729
Synthetic Accessibility Score:	4.992
Fsp3:	0.75
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:	-4.701
MDCK Permeability:	2.2876736693433486e-05
Pgp-inhibitor:	0.975
Pgp-substrate:	0.011
Human Intestinal Absorption (HIA):	0.009
20% Bioavailability (F20%):	0.032
30% Bioavailability (F30%):	0.006

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.972
Plasma Protein Binding (PPB):	80.3961181640625%
Volume Distribution (VD):	1.5
Pgp-substrate:	18.11780548095703%

ADMET: Metabolism

CYP1A2-inhibitor:	0.012
CYP1A2-substrate:	0.582
CYP2C19-inhibitor:	0.138
CYP2C19-substrate:	0.802
CYP2C9-inhibitor:	0.086
CYP2C9-substrate:	0.196
CYP2D6-inhibitor:	0.016
CYP2D6-substrate:	0.058
CYP3A4-inhibitor:	0.828
CYP3A4-substrate:	0.911

ADMET: Excretion

Clearance (CL):	4.423
Half-life (T1/2):	0.509

ADMET: Toxicity

hERG Blockers:	0.017
Human Hepatotoxicity (H-HT):	0.403
Drug-inuced Liver Injury (DILI):	0.035
AMES Toxicity:	0.018
Rat Oral Acute Toxicity:	0.272
Maximum Recommended Daily Dose:	0.249
Skin Sensitization:	0.066
Carcinogencity:	0.924
Eye Corrosion:	0.01
Eye Irritation:	0.107
Respiratory Toxicity:	0.937

Download Data

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

Natural Product: NPC483358

Natural Product ID:	NPC483358
*Common Name:**	VDUVBBMAXXHEQP-SLINCCQESA-M
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	VDUVBBMAXXHEQP-SLINCCQESA-M
Standard InCHI:	InChI=1S/C19H19N3O5S.Na/c1-9-11(12(21-27-9)10-7-5-4-6-8-10)15(23)20-13-16(24)22-14(18(25)26)19(2,3)28-17(13)22;/h4-8,13-14,17H,1-3H3,(H,20,23)(H,25,26);/q;+1/p-1/t13-,14+,17-;/m1./s1
SMILES:	Cc1c(c(c2ccccc2)no1)C(=N[C@@H]1C(=O)N2[C@@H](C(=O)O)C(C)(C)S[C@H]12)[O-].[Na+]
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	23667631
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:0000348] Peptides [CHEMONTID:0004830] Dipeptides

*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
NPO40986	Penicillium janthinellum HK1-6	Strain	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28248508]
NPO40986	Penicillium janthinellum HK1-6	Strain	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30693772]

☑ 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
IC50	4
MIC	42
Others	6

Activity Type	# Activity
Individual Protein	6
Organism	45
SINGLE PROTEIN	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
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]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	>	32.0	ug.mL-1	PMID[17101683]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	0.25	ug.mL-1	PMID[17101683]
NPT73	Individual Protein	Solute carrier organic anion transporter family member 1B1	Homo sapiens	Inhibition	=	76.67	%	PMID[23571415]
NPT72	Individual Protein	Solute carrier organic anion transporter family member 1B3	Homo sapiens	Inhibition	=	90.07	%	PMID[23571415]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	>	128.0	ug.mL-1	PMID[27297569]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	8.0	ug.mL-1	PMID[27297569]
NPT713	Individual Protein	Bile salt export pump	Homo sapiens	IC50	>	133000.0	nM	PMID[23956101]
NPT79	Organism	Bacillus subtilis	Bacillus subtilis	MIC	=	8.0	ug.mL-1	PMID[28633894]
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	=	128.0	ug.mL-1	PMID[28633894]
NPT18	Organism	Pseudomonas aeruginosa	Pseudomonas aeruginosa	MIC	=	128.0	ug.mL-1	PMID[28633894]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	8.0	ug.mL-1	PMID[28633894]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	128.0	ug.mL-1	PMID[28633894]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	>	128.0	ug.mL-1	PMID[28633894]
NPT17	Organism	Staphylococcus epidermidis	Staphylococcus epidermidis	MIC	=	8.0	ug.mL-1	PMID[28633894]
NPT1228	Organism	Streptococcus pyogenes	Streptococcus pyogenes	MIC	=	1.0	ug.mL-1	PMID[28633894]
NPT1228	Organism	Streptococcus pyogenes	Streptococcus pyogenes	MIC	=	2.0	ug.mL-1	PMID[28633894]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	4.0	ug.mL-1	PMID[29657101]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	>	64.0	ug.mL-1	PMID[29657101]
NPT17	Organism	Staphylococcus epidermidis	Staphylococcus epidermidis	MIC	>	64.0	ug.mL-1	PMID[29657101]
NPT1228	Organism	Streptococcus pyogenes	Streptococcus pyogenes	MIC	=	1.0	ug.mL-1	PMID[29657101]
NPT1228	Organism	Streptococcus pyogenes	Streptococcus pyogenes	MIC	>	64.0	ug.mL-1	PMID[29657101]
NPT79	Organism	Bacillus subtilis	Bacillus subtilis	MIC	=	4.0	ug.mL-1	PMID[29657101]
NPT2642	Organism	Bacillus pumilus	Bacillus pumilus	MIC	=	32.0	ug.mL-1	PMID[29657101]
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	>	64.0	ug.mL-1	PMID[29657101]
NPT18	Organism	Pseudomonas aeruginosa	Pseudomonas aeruginosa	MIC	>	64.0	ug.mL-1	PMID[29657101]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	150000.0	nM	PMID[29031065]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	<=	300.0	nM	PMID[29031065]
NPT175	Organism	Enterococcus faecalis	Enterococcus faecalis	MIC	=	9500.0	nM	PMID[29031065]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	>	100.0	ug.mL-1	PMID[28248508]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	0.78	ug.mL-1	PMID[28248508]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	3.13	ug.mL-1	PMID[28248508]
NPT175	Organism	Enterococcus faecalis	Enterococcus faecalis	MIC	=	50.0	ug.mL-1	PMID[28248508]
NPT1531	Organism	Enterococcus faecium	Enterococcus faecium	MIC	>	100.0	ug.mL-1	PMID[28248508]
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	>	100.0	ug.mL-1	PMID[28248508]
NPT20555	ORGANISM	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	3.58	%	DOI[10.21203/rs.3.rs-23951/v1]
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	>	50.0	ug.mL-1	PMID[30693772]
NPT1531	Organism	Enterococcus faecium	Enterococcus faecium	MIC	>	50.0	ug.mL-1	PMID[30693772]
NPT175	Organism	Enterococcus faecalis	Enterococcus faecalis	MIC	>	50.0	ug.mL-1	PMID[30693772]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	0.39	ug.mL-1	PMID[30693772]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	0.2	ug.mL-1	PMID[30693772]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	>	50.0	ug.mL-1	PMID[30693772]
NPT20556	SINGLE PROTEIN	Replicase polyprotein 1ab	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	33.68	%	DOI[10.6019/CHEMBL4495564]
NPT20555	ORGANISM	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	0.08	%	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 NPC483358 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	288
0.1-0.2	2362
0.2-0.3	12548
0.3-0.4	12845
0.4-0.5	11438
0.5-0.6	3076
0.6-0.7	136
0.7-0.8	2
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	2

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 NPC483358 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	166
0.1-0.2	540
0.2-0.3	959
0.3-0.4	1619
0.4-0.5	3934
0.5-0.6	1762
0.6-0.7	155
0.7-0.8	8
0.8-0.85	0
0.85-0.9	0
0.9-0.95	5
0.95-1	2

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