scPDB - 1oyy entry

Protein Data Bank Entry:

PDB ID : 1oyy

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2003-04-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	ATP-dependent DNA helicase RecQ
ID:	RECQ_ECOLI
AC:	P15043
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	3.6.4.12

Chains:

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

Ligand binding site composition:

B-Factor:	70.790
Number of residues:	33
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	MN

Cavity properties

Ligandability	Volume (Å3)
0.413	2072.250

% Hydrophobic	% Polar
30.13	69.87
According to VolSite

Ligand :

HET Code:	AGS
Formula:	C10H14N5O12P3S
Molecular weight:	521.231 g/mol
DrugBank ID:	DB02930
Buried Surface Area:	55.06 %
Polar Surface area:	329.24 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
14.2465	-12.8771	14.4741

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
O2'	OH	TYR- 23	3.02	128.01	H-Bond (Ligand Donor)	false
DuAr	DuAr	TYR- 23	3.56	0	Aromatic Face/Face	false
C2'	CZ	TYR- 23	3.7	0	Hydrophobic	false
N6	O	GLN- 25	3.15	165.42	H-Bond (Ligand Donor)	false
O4'	NH1	ARG- 27	2.96	135.62	H-Bond (Protein Donor)	false
DuAr	CZ	ARG- 27	3.48	17.96	Pi/Cation	false
N7	NE2	GLN- 30	2.87	155.79	H-Bond (Protein Donor)	false
N6	OE1	GLN- 30	2.5	144.63	H-Bond (Ligand Donor)	false
O2G	N	GLY- 50	3.02	165.13	H-Bond (Protein Donor)	false
O1B	N	GLY- 52	2.7	153.51	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 53	3.21	163.74	H-Bond (Protein Donor)	false
O1B	N	LYS- 53	3.03	133.88	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 53	2.85	135.31	H-Bond (Protein Donor)	false
O2B	N	LYS- 53	2.98	139.05	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 53	3.21	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 53	3.8	0	Ionic (Protein Cationic)	false
O1B	NZ	LYS- 53	2.85	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 53	3.56	0	Ionic (Protein Cationic)	false
O1A	N	SER- 54	2.67	171.7	H-Bond (Protein Donor)	false
O1A	OG	SER- 54	2.54	145.46	H-Bond (Protein Donor)	false
O2B	MN	MN- 526	2.43	0	Metal Acceptor	false