scPDB - 4k4o entry

Protein Data Bank Entry:

PDB ID : 4k4o

Resolution :1.300 Å

Experimental Method : X-ray

Deposition Date : 2013-04-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	DNA gyrase subunit B
ID:	GYRB_ENTFA
AC:	Q839Z1
Organism:	Enterococcus faecalis
Reign:	Bacteria
TaxID:	226185
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	9.449
Number of residues:	27
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.334	249.750

% Hydrophobic	% Polar
52.70	47.30
According to VolSite

Ligand :

HET Code:	DOO
Formula:	C22H24FN8O
Molecular weight:	435.477 g/mol
DrugBank ID:	-
Buried Surface Area:	59.68 %
Polar Surface area:	108.46 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	3
Rings:	6
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
10.2371	-5.15884	14.8839

Binding mode :

What is Poseview ?

2D View
3D View

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
F30	CD1	ILE- 45	3.96	0	Hydrophobic	false
C1	CG2	ILE- 45	4.03	0	Hydrophobic	false
C32	CG2	ILE- 45	4.08	0	Hydrophobic	false
C7	CB	ASN- 48	4.43	0	Hydrophobic	false
C23	CB	ASN- 48	4.43	0	Hydrophobic	false
C5	CB	ASN- 48	3.38	0	Hydrophobic	false
C32	CG1	VAL- 73	3.72	0	Hydrophobic	false
N9	OD1	ASP- 75	2.79	155.47	H-Bond (Ligand Donor)	false
N31	OD1	ASP- 75	2.96	168.23	H-Bond (Ligand Donor)	false
DuAr	CZ	ARG- 78	3.55	167.18	Pi/Cation	false
C26	CG2	ILE- 80	4.14	0	Hydrophobic	false
C5	CD1	ILE- 80	3.75	0	Hydrophobic	false
C7	CG1	ILE- 80	3.36	0	Hydrophobic	false
C21	CG	PRO- 81	3.86	0	Hydrophobic	false
C5	CG1	VAL- 96	4.44	0	Hydrophobic	false
C26	CG2	VAL- 96	4.25	0	Hydrophobic	false
C23	CG1	VAL- 96	4.17	0	Hydrophobic	false
F30	CE1	PHE- 97	3.57	0	Hydrophobic	false
F30	CB	SER- 122	3.63	0	Hydrophobic	false
C32	CG2	THR- 167	4.28	0	Hydrophobic	false
C2	CG2	THR- 167	3.65	0	Hydrophobic	false
C3	CG2	THR- 167	3.68	0	Hydrophobic	false
C32	CG2	VAL- 169	4.13	0	Hydrophobic	false
C1	CG2	VAL- 169	3.65	0	Hydrophobic	false
N10	O	HOH- 415	2.8	153.04	H-Bond (Protein Donor)	false