NPASS Compound

Structure

NPC55938 OpenBabel06302216192D 33 39 0 0 1 0 0 0 0 0999 V2000 -2.0040 0.4369 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8907 0.7290 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.4726 1.8014 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0944 2.7699 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.6765 1.7351 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.6450 2.3570 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8310 3.4928 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9076 3.8997 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7983 3.1707 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6124 2.0348 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5357 1.6280 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1176 0.5556 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.9946 -0.3310 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4135 -0.4103 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.9258 -1.5075 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8720 -1.8313 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.4602 -1.7467 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 4.1364 -2.6928 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9353 -0.6742 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.4668 0.5443 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9538 0.8404 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 3.9538 1.4328 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4408 1.7290 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4408 2.3213 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9538 2.6175 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4668 2.3213 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4668 1.7290 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9798 1.4328 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9766 2.0083 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.9798 0.8404 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2.5497 -0.5968 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9685 0.6218 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 0 0 0 2 3 1 0 0 0 0 2 33 1 0 0 0 0 3 4 2 0 0 0 0 3 5 1 0 0 0 0 5 32 1 0 0 0 0 5 6 1 0 0 0 0 6 11 2 0 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 8 9 1 0 0 0 0 9 10 2 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 12 31 1 0 0 0 0 12 13 1 1 0 0 0 12 32 1 0 0 0 0 14 13 1 6 0 0 0 14 15 1 0 0 0 0 14 30 1 0 0 0 0 15 16 2 0 0 0 0 15 17 1 0 0 0 0 17 18 1 0 0 0 0 17 19 1 0 0 0 0 19 20 1 1 0 0 0 19 31 1 0 0 0 0 20 30 1 0 0 0 0 20 21 2 0 0 0 0 21 22 1 0 0 0 0 22 27 2 0 0 0 0 22 23 1 0 0 0 0 23 24 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 1 0 0 0 0 28 29 2 0 0 0 0 28 30 1 0 0 0 0 32 33 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	443.16
Volume:	427.545
LogP:	0.795
LogD:	0.998
LogS:	-3.561
# Rotatable Bonds:	0
TPSA:	96.77
# H-Bond Aceptor:	9
# H-Bond Donor:	1
# Rings:	8
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.564
Synthetic Accessibility Score:	5.721
Fsp3:	0.333
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:	-5.399
MDCK Permeability:	2.499792208254803e-05
Pgp-inhibitor:	0.427
Pgp-substrate:	0.479
Human Intestinal Absorption (HIA):	0.011
20% Bioavailability (F20%):	0.062
30% Bioavailability (F30%):	0.103

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.131
Plasma Protein Binding (PPB):	59.27167510986328%
Volume Distribution (VD):	1.733
Pgp-substrate:	46.77842712402344%

ADMET: Metabolism

CYP1A2-inhibitor:	0.025
CYP1A2-substrate:	0.567
CYP2C19-inhibitor:	0.041
CYP2C19-substrate:	0.807
CYP2C9-inhibitor:	0.098
CYP2C9-substrate:	0.152
CYP2D6-inhibitor:	0.007
CYP2D6-substrate:	0.197
CYP3A4-inhibitor:	0.299
CYP3A4-substrate:	0.934

ADMET: Excretion

Clearance (CL):	3.127
Half-life (T1/2):	0.15

ADMET: Toxicity

hERG Blockers:	0.01
Human Hepatotoxicity (H-HT):	0.951
Drug-inuced Liver Injury (DILI):	0.983
AMES Toxicity:	0.225
Rat Oral Acute Toxicity:	0.338
Maximum Recommended Daily Dose:	0.926
Skin Sensitization:	0.803
Carcinogencity:	0.923
Eye Corrosion:	0.003
Eye Irritation:	0.007
Respiratory Toxicity:	0.905

Download Data

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

Natural Product: NPC55938

Natural Product ID:	NPC55938
*Common Name:**	BOZGEGDMHAOPIQ-JBGRHRSXSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	BOZGEGDMHAOPIQ-JBGRHRSXSA-N
Standard InCHI:	InChI=1S/C24H21N5O4/c1-12-19(30)29-16-10-6-4-8-14(16)24(23(29)25-12)11-17-21(32)27(2)22(33-24)18-26-15-9-5-3-7-13(15)20(31)28(17)18/h3-10,12,17,22-23,25H,11H2,1-2H3/t12-,17-,22-,23-,24-/m0/s1
SMILES:	C[C@H]1C(=O)N2c3ccccc3[C@@]3(C[C@H]4C(=O)N(C)[C@H](c5nc6ccccc6c(=O)n45)O3)[C@H]2N1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	124785416
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:0000347] Amino acids and derivatives [CHEMONTID:0000060] Alpha amino acids and derivatives [CHEMONTID:0002309] Alpha amino acid amides

*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
NPO12970	Aspergillus fischeri	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31920082]
NPO12970	Aspergillus fischeri	Species	Aspergillaceae	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	6

Activity Type	# Activity
Organism	6

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	=	8.0	ug.mL-1	PMID[31920082]
NPT747	Organism	Acinetobacter baumannii	Acinetobacter baumannii	MIC	=	32.0	ug.mL-1	PMID[31920082]
NPT18	Organism	Pseudomonas aeruginosa	Pseudomonas aeruginosa	MIC	=	32.0	ug.mL-1	PMID[31920082]
NPT173	Organism	Klebsiella pneumoniae	Klebsiella pneumoniae	MIC	>=	100.0	ug.mL-1	PMID[31920082]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	>=	100.0	ug.mL-1	PMID[31920082]
NPT175	Organism	Enterococcus faecalis	Enterococcus faecalis	MIC	=	16.0	ug.mL-1	PMID[31920082]

☑ 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 NPC55938 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	516
0.1-0.2	3410
0.2-0.3	13707
0.3-0.4	17070
0.4-0.5	3646
0.5-0.6	3114
0.6-0.7	1115
0.7-0.8	79
0.8-0.85	10
0.85-0.9	22
0.9-0.95	6
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 NPC55938 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	246
0.1-0.2	610
0.2-0.3	905
0.3-0.4	1694
0.4-0.5	2483
0.5-0.6	2104
0.6-0.7	1015
0.7-0.8	93
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