scPDB - 4duh entry

Protein Data Bank Entry:

PDB ID : 4duh

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 2012-02-22

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:	25.128
Number of residues:	28
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.787	438.750

% Hydrophobic	% Polar
50.77	49.23
According to VolSite

Ligand :

HET Code:	RLI
Formula:	C17H15N4O3S2
Molecular weight:	387.456 g/mol
DrugBank ID:	-
Buried Surface Area:	62.77 %
Polar Surface area:	163.52 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	2
Rings:	3
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
30.6548	4.82127	4.88004

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
C11	CG1	VAL- 43	3.6	0	Hydrophobic	false
S10	CB	ASN- 46	3.85	0	Hydrophobic	false
C13	CB	ALA- 47	4.06	0	Hydrophobic	false
C16	CG	GLU- 50	3.85	0	Hydrophobic	false
C11	CG1	VAL- 71	4.25	0	Hydrophobic	false
N10	OD1	ASP- 73	2.83	159.67	H-Bond (Ligand Donor)	false
C23	CD	ARG- 76	4.46	0	Hydrophobic	false
S10	CG1	ILE- 78	3.66	0	Hydrophobic	false
C16	CG1	ILE- 78	4.47	0	Hydrophobic	false
C27	CG	PRO- 79	3.67	0	Hydrophobic	false
S11	CD1	ILE- 94	3.6	0	Hydrophobic	false
N13	O	GLY- 101	2.78	165.59	H-Bond (Ligand Donor)	false
S11	CG	LYS- 103	4.13	0	Hydrophobic	false
O11	NH1	ARG- 136	2.81	148.42	H-Bond (Protein Donor)	false
O11	NH2	ARG- 136	2.93	141.31	H-Bond (Protein Donor)	false
O11	CZ	ARG- 136	3.29	0	Ionic (Protein Cationic)	false
C11	CG2	THR- 165	3.86	0	Hydrophobic	false
C11	CG2	VAL- 167	3.84	0	Hydrophobic	false
N11	O	HOH- 451	2.89	160.07	H-Bond (Protein Donor)	false