scPDB - 3lps entry

Protein Data Bank Entry:

PDB ID : 3lps

Resolution :2.290 Å

Experimental Method : X-ray

Deposition Date : 2010-02-05

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:	Q5GYJ8_XANOR
AC:	Q5GYJ8
Organism:	Xanthomonas oryzae pv. oryzae
Reign:	Bacteria
TaxID:	291331
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	26.878
Number of residues:	28
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.402	297.000

% Hydrophobic	% Polar
52.27	47.73
According to VolSite

Ligand :

HET Code:	NOV
Formula:	C31H35N2O11
Molecular weight:	611.616 g/mol
DrugBank ID:	DB01051
Buried Surface Area:	43.11 %
Polar Surface area:	198.92 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	4
Rings:	4
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
-5.95223	26.8391	63.0447

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
C1	CB	ASN- 86	4.11	0	Hydrophobic	false
C27	CB	ASN- 86	4.13	0	Hydrophobic	false
O6	O	ASN- 86	2.71	172.13	H-Bond (Ligand Donor)	false
O6	ND2	ASN- 86	3.42	150.57	H-Bond (Protein Donor)	false
C29	CG	GLU- 90	4.09	0	Hydrophobic	false
N1	OD2	ASP- 113	2.78	168.68	H-Bond (Ligand Donor)	false
C2	CB	ARG- 116	4.08	0	Hydrophobic	false
DuAr	CZ	ARG- 116	3.8	153.81	Pi/Cation	false
C1	CE	MET- 118	3.66	0	Hydrophobic	false
C28	CG	MET- 118	4.4	0	Hydrophobic	false
C16	CG	PRO- 119	4.16	0	Hydrophobic	false
C19	CG	PRO- 119	4.45	0	Hydrophobic	false
C17	CB	PRO- 119	3.68	0	Hydrophobic	false
O3	OD1	ASP- 121	3.11	145.16	H-Bond (Ligand Donor)	false
O3	OD2	ASP- 121	2.69	142.12	H-Bond (Ligand Donor)	false
C1	CG2	ILE- 134	4.34	0	Hydrophobic	false
C23	CD1	ILE- 134	3.92	0	Hydrophobic	false
C24	CD1	ILE- 134	4.39	0	Hydrophobic	false
C1	CG1	VAL- 160	4	0	Hydrophobic	false
O10	NH1	ARG- 176	3.35	143.79	H-Bond (Protein Donor)	false
O11	NH1	ARG- 176	2.91	138.44	H-Bond (Protein Donor)	false
O11	NH2	ARG- 176	2.71	149.64	H-Bond (Protein Donor)	false