scPDB - 4lpb entry

Protein Data Bank Entry:

PDB ID : 4lpb

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 2013-07-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	DNA topoisomerase 4 subunit B
ID:	Q8DQB5_STRR6
AC:	Q8DQB5
Organism:	Streptococcus pneumoniae
Reign:	Bacteria
TaxID:	171101
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	17.956
Number of residues:	28
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.013	259.875

% Hydrophobic	% Polar
42.86	57.14
According to VolSite

Ligand :

HET Code:	1YP
Formula:	C19H14F3N7O3S
Molecular weight:	477.420 g/mol
DrugBank ID:	-
Buried Surface Area:	52.95 %
Polar Surface area:	158.72 Å2

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

Mass center Coordinates

X	Y	Z
14.3918	29.0739	7.33982

Binding mode :

What is Poseview ?

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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
C1	CG2	ILE- 48	3.99	0	Hydrophobic	false
C1	CB	ALA- 52	4.43	0	Hydrophobic	false
C1	CG1	VAL- 76	3.94	0	Hydrophobic	false
N1	OD2	ASP- 78	2.84	154.54	H-Bond (Ligand Donor)	false
N2	OD2	ASP- 78	2.94	150.54	H-Bond (Ligand Donor)	false
C10	CB	ARG- 81	4.47	0	Hydrophobic	false
C11	CD	ARG- 81	4.42	0	Hydrophobic	false
DuAr	CZ	ARG- 81	3.87	154.71	Pi/Cation	false
S1	CE	MET- 83	4.15	0	Hydrophobic	false
C5	CG	MET- 83	3.57	0	Hydrophobic	false
C11	CG	PRO- 84	4.47	0	Hydrophobic	false
F2	CG	PRO- 84	3.35	0	Hydrophobic	false
F2	CG2	THR- 94	3.96	0	Hydrophobic	false
F2	CD1	ILE- 98	3.67	0	Hydrophobic	false
N6	NH2	ARG- 140	3.5	145.57	H-Bond (Protein Donor)	false
N6	NH1	ARG- 140	3.35	153.04	H-Bond (Protein Donor)	false
N5	NH1	ARG- 140	3.04	156.38	H-Bond (Protein Donor)	false
C1	CG2	THR- 172	4.24	0	Hydrophobic	false
C1	CG2	VAL- 174	3.89	0	Hydrophobic	false
N3	O	HOH- 402	2.75	149.75	H-Bond (Protein Donor)	false
O1	O	HOH- 424	2.85	179.97	H-Bond (Protein Donor)	false