scPDB - 4ksh entry

Protein Data Bank Entry:

PDB ID : 4ksh

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2013-05-17

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:	21.067
Number of residues:	31
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.752	330.750

% Hydrophobic	% Polar
50.00	50.00
According to VolSite

Ligand :

HET Code:	HTT
Formula:	C20H22ClN7OS
Molecular weight:	443.953 g/mol
DrugBank ID:	-
Buried Surface Area:	57.65 %
Polar Surface area:	136.94 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	2
Rings:	5
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
-10.0533	-6.11983	-15.4584

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
C6	CG2	ILE- 45	3.78	0	Hydrophobic	false
CL8	CB	ASN- 48	3.34	0	Hydrophobic	false
C6	CB	ASN- 48	4.29	0	Hydrophobic	false
C3	CB	ASN- 48	4.18	0	Hydrophobic	false
C14	CB	ASN- 48	4.17	0	Hydrophobic	false
N18	OD1	ASN- 48	2.85	155.96	H-Bond (Ligand Donor)	false
S19	CG	GLU- 52	3.7	0	Hydrophobic	false
C7	CG1	VAL- 73	4.3	0	Hydrophobic	false
N1	OD1	ASP- 75	2.69	163.06	H-Bond (Ligand Donor)	false
DuAr	CZ	ARG- 78	3.71	23.07	Pi/Cation	false
DuAr	CZ	ARG- 78	3.65	20.97	Pi/Cation	false
C21	CB	ARG- 78	3.72	0	Hydrophobic	false
CL8	CD1	ILE- 80	4.04	0	Hydrophobic	false
C3	CG1	ILE- 80	3.41	0	Hydrophobic	false
C17	CG2	ILE- 80	3.9	0	Hydrophobic	false
C21	CG	PRO- 81	4.26	0	Hydrophobic	false
C27	CG	PRO- 81	4.1	0	Hydrophobic	false
C14	CG1	VAL- 96	4.05	0	Hydrophobic	false
C16	CG2	VAL- 96	4.16	0	Hydrophobic	false
CL8	CZ	PHE- 97	4.47	0	Hydrophobic	false
CL8	CB	SER- 122	4.38	0	Hydrophobic	false
O30	NZ	LYS- 138	2.95	134.26	H-Bond (Protein Donor)	false
C7	CG2	THR- 167	3.75	0	Hydrophobic	false
C7	CG2	VAL- 169	3.71	0	Hydrophobic	false
N12	O	HOH- 407	2.77	147.32	H-Bond (Protein Donor)	false