scPDB - 4kfg entry

Protein Data Bank Entry:

PDB ID : 4kfg

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2013-04-26

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_ECOLI
AC:	P0AES6
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	19.129
Number of residues:	33
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.220	337.500

% Hydrophobic	% Polar
47.00	53.00
According to VolSite

Ligand :

HET Code:	DOO
Formula:	C22H24FN8O
Molecular weight:	435.477 g/mol
DrugBank ID:	-
Buried Surface Area:	58.04 %
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
-1.01063	21.2041	-21.2337

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	CG1	VAL- 43	4.38	0	Hydrophobic	false
C1	CG1	VAL- 43	4.03	0	Hydrophobic	false
C32	CG1	VAL- 43	4.18	0	Hydrophobic	false
C23	CB	ASN- 46	4.46	0	Hydrophobic	false
C6	CB	ASN- 46	3.33	0	Hydrophobic	false
C32	CB	ALA- 47	3.86	0	Hydrophobic	false
C32	CG1	VAL- 71	3.63	0	Hydrophobic	false
N9	OD1	ASP- 73	2.73	161.62	H-Bond (Ligand Donor)	false
N31	OD1	ASP- 73	2.98	168.11	H-Bond (Ligand Donor)	false
C15	CB	ARG- 76	4.37	0	Hydrophobic	false
DuAr	CZ	ARG- 76	3.51	176.33	Pi/Cation	false
C7	CG1	ILE- 78	3.55	0	Hydrophobic	false
C4	CD1	ILE- 78	3.79	0	Hydrophobic	false
C23	CG2	ILE- 90	4	0	Hydrophobic	false
C26	CD1	ILE- 90	3.91	0	Hydrophobic	false
F30	CE	MET- 91	3.78	0	Hydrophobic	false
F30	CG2	VAL- 120	3.47	0	Hydrophobic	false
C32	CG2	THR- 165	4.47	0	Hydrophobic	false
C2	CG2	THR- 165	3.57	0	Hydrophobic	false
C3	CG2	THR- 165	3.55	0	Hydrophobic	false
C1	CG2	VAL- 167	3.85	0	Hydrophobic	false
N10	O	HOH- 414	2.82	179.96	H-Bond (Protein Donor)	false
N19	O	HOH- 445	2.93	179.95	H-Bond (Protein Donor)	false