scPDB - 5bnt entry

Protein Data Bank Entry:

PDB ID : 5bnt

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2015-05-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Aspartate-semialdehyde dehydrogenase
ID:	DHAS_PSEAE
AC:	Q51344
Organism:	Pseudomonas aeruginosa
Reign:	Bacteria
TaxID:	208964
EC Number:	1.2.1.11

Chains:

Chain Name:	Percentage of Residues within binding site
B	93 %
C	7 %

Ligand binding site composition:

B-Factor:	35.059
Number of residues:	30
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.341	482.625

% Hydrophobic	% Polar
27.97	72.03
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	39.71 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
-16.7539	28.5265	6.76803

Binding mode :

What is Poseview ?

2D View
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Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
O1X	CZ	ARG- 10	3.94	0	Ionic (Protein Cationic)	false
O3X	CZ	ARG- 10	3.27	0	Ionic (Protein Cationic)	false
O1X	NH2	ARG- 10	2.98	163.03	H-Bond (Protein Donor)	false
O3X	NH2	ARG- 10	3.17	127.23	H-Bond (Protein Donor)	false
O3X	NE	ARG- 10	2.54	162.58	H-Bond (Protein Donor)	false
DuAr	CZ	ARG- 10	3.65	20.34	Pi/Cation	false
O2A	N	MET- 12	2.91	165.41	H-Bond (Protein Donor)	false
O2N	N	VAL- 13	2.54	173.99	H-Bond (Protein Donor)	false
O2X	OG1	THR- 37	3.16	173.73	H-Bond (Protein Donor)	false
O2X	N	THR- 37	2.92	148.81	H-Bond (Protein Donor)	false
O1X	OG	SER- 38	2.74	160.06	H-Bond (Protein Donor)	false
O3B	OE1	GLN- 73	2.75	122.27	H-Bond (Ligand Donor)	false
O2B	NE2	GLN- 73	3.34	153.6	H-Bond (Protein Donor)	false
O2X	O	HOH- 677	2.97	179.94	H-Bond (Protein Donor)	false