NPASS Compound

Structure

NPC489607 OpenBabel06302215502D 33 35 0 0 1 0 0 0 0 0999 V2000 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 2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 1.5000 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 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 1 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 1.7321 2.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 1 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 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -3.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -3.0000 0.0000 N 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 N 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 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -1.0000 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 -0.8660 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -2.5000 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 -0.0000 -1.0000 0.0000 C 0 0 0 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 0.0000 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 4.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 4 7 1 0 0 0 0 5 6 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 8 33 1 1 0 0 0 9 10 2 3 0 0 0 9 32 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 1 0 0 0 11 19 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 16 18 1 0 0 0 0 19 20 2 3 0 0 0 19 31 1 0 0 0 0 20 21 1 0 0 0 0 21 30 2 0 0 0 0 21 22 1 0 0 0 0 22 23 2 0 0 0 0 23 24 1 0 0 0 0 24 29 2 0 0 0 0 24 25 1 0 0 0 0 25 26 2 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 28 29 1 0 0 0 0 29 30 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	446.24
Volume:	469.847
LogP:	2.009
LogD:	1.431
LogS:	-2.706
# Rotatable Bonds:	13
TPSA:	146.12
# H-Bond Aceptor:	8
# H-Bond Donor:	8
# Rings:	3
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.16
Synthetic Accessibility Score:	2.894
Fsp3:	0.24
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.072
MDCK Permeability:	2.3707802029093727e-05
Pgp-inhibitor:	0.038
Pgp-substrate:	0.145
Human Intestinal Absorption (HIA):	0.952
20% Bioavailability (F20%):	0.939
30% Bioavailability (F30%):	0.993

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.174
Plasma Protein Binding (PPB):	88.95419311523438%
Volume Distribution (VD):	0.903
Pgp-substrate:	15.667154312133789%

ADMET: Metabolism

CYP1A2-inhibitor:	0.087
CYP1A2-substrate:	0.079
CYP2C19-inhibitor:	0.156
CYP2C19-substrate:	0.06
CYP2C9-inhibitor:	0.079
CYP2C9-substrate:	0.034
CYP2D6-inhibitor:	0.775
CYP2D6-substrate:	0.549
CYP3A4-inhibitor:	0.632
CYP3A4-substrate:	0.138

ADMET: Excretion

Clearance (CL):	9.526
Half-life (T1/2):	0.572

ADMET: Toxicity

hERG Blockers:	0.514
Human Hepatotoxicity (H-HT):	0.242
Drug-inuced Liver Injury (DILI):	0.134
AMES Toxicity:	0.821
Rat Oral Acute Toxicity:	0.675
Maximum Recommended Daily Dose:	0.83
Skin Sensitization:	0.468
Carcinogencity:	0.078
Eye Corrosion:	0.003
Eye Irritation:	0.005
Respiratory Toxicity:	0.899

Download Data

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

Natural Product: NPC489607

Natural Product ID:	NPC489607
*Common Name:**	ZNHUFUZDUQRKBB-VXKWHMMOSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	ZNHUFUZDUQRKBB-VXKWHMMOSA-N
Standard InCHI:	InChI=1S/C25H30N6O2/c26-21(15-17-7-2-1-3-8-17)23(32)31-22(11-6-14-29-25(27)28)24(33)30-20-13-12-18-9-4-5-10-19(18)16-20/h1-5,7-10,12-13,16,21-22H,6,11,14-15,26H2,(H,30,33)(H,31,32)(H4,27,28,29)/t21-,22-/m0/s1
SMILES:	c1ccc(cc1)C[C@@H](C(=N[C@@H](CCCNC(=N)N)C(=Nc1ccc2ccccc2c1)O)O)N
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	443301
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
NPO40304	Pseudoalteromonas sp.	Species	Pseudoalteromonadaceae	Bacteria	n.a.	n.a.	n.a.	PMID[25646964]

☑ 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	1
LD50	1
MIC	78
Others	71

Activity Type	# Activity
Individual Protein	1
NON-MOLECULAR	3
Organism	85
Others	61
SINGLE PROTEIN	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT5885	Individual Protein	Phospho-N-acetylmuramoyl-pentapeptide-transferase	Escherichia coli K-12	IC50	=	730000.0	nM	PMID[11459657]
NPT18	Organism	Pseudomonas aeruginosa	Pseudomonas aeruginosa	MIC	>	512.0	ug.mL-1	PMID[12873508]
NPT27	Others	Unspecified		LD50	<	25.0	mg.kg-1	PMID[12873508]
NPT18	Organism	Pseudomonas aeruginosa	Pseudomonas aeruginosa	MIC	>	512.0	ug.mL-1	PMID[11266165]
NPT18	Organism	Pseudomonas aeruginosa	Pseudomonas aeruginosa	MIC	>	512.0	ug.mL-1	PMID[10585202]
NPT18	Organism	Pseudomonas aeruginosa	Pseudomonas aeruginosa	MIC	=	2.0	ug.mL-1	PMID[10585202]
NPT18	Organism	Pseudomonas aeruginosa	Pseudomonas aeruginosa	MIC	=	1.0	ug.mL-1	PMID[10585202]
NPT18	Organism	Pseudomonas aeruginosa	Pseudomonas aeruginosa	MIC	=	0.5	ug.mL-1	PMID[10585202]
NPT18	Organism	Pseudomonas aeruginosa	Pseudomonas aeruginosa	MIC	=	0.125	ug.mL-1	PMID[10585202]
NPT18	Organism	Pseudomonas aeruginosa	Pseudomonas aeruginosa	MIC	=	0.06	ug.mL-1	PMID[10585202]
NPT18	Organism	Pseudomonas aeruginosa	Pseudomonas aeruginosa	MIC	=	4.0	ug.mL-1	PMID[10585202]
NPT18	Organism	Pseudomonas aeruginosa	Pseudomonas aeruginosa	MIC	=	0.25	ug.mL-1	PMID[10585202]
NPT18	Organism	Pseudomonas aeruginosa	Pseudomonas aeruginosa	MIC	=	0.03	ug.mL-1	PMID[10585202]
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	=	256.0	ug.mL-1	PMID[11459657]
NPT2	Others	Unspecified		FC	=	3.0	n.a.	PMID[17606685]
NPT19518	SINGLE PROTEIN	CmeA	Campylobacter jejuni	FC	=	2.0	n.a.	PMID[17606685]
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	=	64.0	ug.mL-1	PMID[20160051]
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	>	256.0	ug.mL-1	PMID[20160051]
NPT1140	Organism	Escherichia coli ATCC 8739	Escherichia coli ATCC 8739	MIC	>	256.0	ug.mL-1	PMID[20160051]
NPT173	Organism	Klebsiella pneumoniae	Klebsiella pneumoniae	MIC	=	256.0	ug.mL-1	PMID[20160051]
NPT720	Organism	Enterobacter aerogenes	Enterobacter aerogenes	MIC	>	256.0	ug.mL-1	PMID[20160051]
NPT173	Organism	Klebsiella pneumoniae	Klebsiella pneumoniae	MIC	>	256.0	ug.mL-1	PMID[20160051]
NPT1548	Organism	Pseudomonas aeruginosa PAO1	Pseudomonas aeruginosa PAO1	MIC	>	256.0	ug.mL-1	PMID[20160051]
NPT18	Organism	Pseudomonas aeruginosa	Pseudomonas aeruginosa	MIC	>	256.0	ug.mL-1	PMID[20160051]
NPT1033	Organism	Enterobacter cloacae	Enterobacter cloacae	MIC	>	256.0	ug.mL-1	PMID[20160051]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	MIC	=	256.0	ug.mL-1	PMID[18086833]
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	>	256.0	ug.mL-1	PMID[18086833]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	MIC	>	256.0	ug.mL-1	PMID[18086833]
NPT2	Others	Unspecified		Activity	=	0.012	ug ml-1	PMID[19104017]
NPT2	Others	Unspecified		Activity	=	0.023	ug ml-1	PMID[19104017]
NPT2	Others	Unspecified		Activity	=	0.032	ug ml-1	PMID[19104017]
NPT2	Others	Unspecified		Activity	=	0.38	ug ml-1	PMID[19104017]
NPT2	Others	Unspecified		Activity	=	0.5	ug ml-1	PMID[19104017]
NPT2	Others	Unspecified		Activity	=	1.0	ug ml-1	PMID[19104017]
NPT2	Others	Unspecified		Activity	=	0.75	ug ml-1	PMID[19104017]
NPT2	Others	Unspecified		Activity	=	2.0	ug ml-1	PMID[19104017]
NPT2	Others	Unspecified		Activity	=	0.094	ug ml-1	PMID[19104017]
NPT2	Others	Unspecified		Activity	=	0.19	ug ml-1	PMID[19104017]
NPT2	Others	Unspecified		Activity	=	3.0	ug ml-1	PMID[19104017]
NPT2	Others	Unspecified		Activity	=	0.008	ug ml-1	PMID[19104017]
NPT2	Others	Unspecified		Activity	=	0.064	ug ml-1	PMID[19104017]
NPT2	Others	Unspecified		Activity	=	16.0	ug ml-1	PMID[19104017]
NPT2	Others	Unspecified		Activity	=	24.0	ug ml-1	PMID[19104017]
NPT2	Others	Unspecified		Activity	=	32.0	ug ml-1	PMID[19104017]
NPT2	Others	Unspecified		Activity	=	256.0	ug ml-1	PMID[19104017]
NPT2	Others	Unspecified		FC	=	2.7	n.a.	PMID[19687245]
NPT2	Others	Unspecified		FC	=	3.2	n.a.	PMID[19687245]
NPT2	Others	Unspecified		FC	=	4.0	n.a.	PMID[19687245]
NPT2	Others	Unspecified		FC	=	8.0	n.a.	PMID[19687245]
NPT2	Others	Unspecified		FC	=	2.5	n.a.	PMID[19687245]
NPT2	Others	Unspecified		FC	=	3.3	n.a.	PMID[19687245]
NPT2	Others	Unspecified		FC	=	5.0	n.a.	PMID[19687245]
NPT2	Others	Unspecified		FC	=	1.7	n.a.	PMID[19687245]
NPT2908	Organism	Streptomyces coelicolor	Streptomyces coelicolor	MIC	=	200.0	ug.mL-1	PMID[19687245]
NPT2	Others	Unspecified		Inhibition	=	60.0	%	PMID[20606071]
NPT2908	Organism	Streptomyces coelicolor	Streptomyces coelicolor	FC	=	2.6	n.a.	PMID[22055717]
NPT2908	Organism	Streptomyces coelicolor	Streptomyces coelicolor	MIC	=	25.0	ug.mL-1	PMID[22055717]
NPT720	Organism	Enterobacter aerogenes	Enterobacter aerogenes	MIC	=	5000000.0	nM	PMID[23218781]
NPT566	Organism	Salmonella typhimurium	Salmonella enterica subsp. enterica serovar Typhimurium	Ratio	=	64.0	n.a.	PMID[23352753]
NPT566	Organism	Salmonella typhimurium	Salmonella enterica subsp. enterica serovar Typhimurium	Ratio	=	8.0	n.a.	PMID[23352753]
NPT720	Organism	Enterobacter aerogenes	Enterobacter aerogenes	Ratio	=	8.0	n.a.	PMID[23352753]
NPT720	Organism	Enterobacter aerogenes	Enterobacter aerogenes	Ratio	=	16.0	n.a.	PMID[23352753]
NPT566	Organism	Salmonella typhimurium	Salmonella enterica subsp. enterica serovar Typhimurium	MIC	=	150000.0	nM	PMID[23352753]
NPT566	Organism	Salmonella typhimurium	Salmonella enterica subsp. enterica serovar Typhimurium	MIC	=	1215000.0	nM	PMID[23352753]
NPT720	Organism	Enterobacter aerogenes	Enterobacter aerogenes	MIC	=	150000.0	nM	PMID[23352753]
NPT720	Organism	Enterobacter aerogenes	Enterobacter aerogenes	MIC	=	2430000.0	nM	PMID[23352753]
NPT2	Others	Unspecified		MIC	=	16.0	ug.mL-1	PMID[28129976]
NPT2	Others	Unspecified		MIC	=	2.0	ug.mL-1	PMID[28129976]
NPT2	Others	Unspecified		MIC	=	128.0	ug.mL-1	PMID[28129976]
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	=	1.0	ug.mL-1	PMID[28129976]
NPT2	Others	Unspecified		MIC	=	2.0	ug.mL-1	PMID[28594170]
NPT19	Organism	Escherichia coli	Escherichia coli	FC	=	4.0	n.a.	PMID[31173969]
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	=	16.0	ug.mL-1	PMID[31173969]
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	>	100.0	ug.mL-1	PMID[31173969]
NPT19	Organism	Escherichia coli	Escherichia coli	FC	=	4.0	n.a.	PMID[31235265]
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	>	200.0	ug.mL-1	PMID[31235265]
NPT720	Organism	Enterobacter aerogenes	Enterobacter aerogenes	Ratio	=	8.0	n.a.	PMID[32840108]
NPT720	Organism	Enterobacter aerogenes	Enterobacter aerogenes	Ratio	=	16.0	n.a.	PMID[32840108]
NPT566	Organism	Salmonella typhimurium	Salmonella enterica subsp. enterica serovar Typhimurium	Ratio	=	8.0	n.a.	PMID[32840108]
NPT566	Organism	Salmonella typhimurium	Salmonella enterica subsp. enterica serovar Typhimurium	Ratio	=	64.0	n.a.	PMID[32840108]
NPT566	Organism	Salmonella typhimurium	Salmonella enterica subsp. enterica serovar Typhimurium	Ratio	=	16.0	n.a.	PMID[32840108]
NPT2	Others	Unspecified		Activity	=	25.0	%	PMID[32840108]
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	=	256.0	ug.mL-1	PMID[29220791]
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	=	2.0	ug.mL-1	PMID[29220791]
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	=	16.0	ug.mL-1	PMID[29220791]

☑ 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 NPC489607 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	296
0.1-0.2	2886
0.2-0.3	14553
0.3-0.4	16308
0.4-0.5	5710
0.5-0.6	2670
0.6-0.7	268
0.7-0.8	5
0.8-0.85	0
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 NPC489607 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	164
0.1-0.2	480
0.2-0.3	1127
0.3-0.4	1212
0.4-0.5	3463
0.5-0.6	2376
0.6-0.7	308
0.7-0.8	20
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