scPDB - 4pds entry

Protein Data Bank Entry:

PDB ID : 4pds

Resolution :2.900 Å

Experimental Method : X-ray

Deposition Date : 2014-04-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Serine/threonine-protein kinase RAD53
ID:	RAD53_YEAST
AC:	P22216
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	2.7.12.1

Chains:

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

Ligand binding site composition:

B-Factor:	91.636
Number of residues:	21
Including
Standard Amino Acids:	21
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.488	550.125

% Hydrophobic	% Polar
63.19	36.81
According to VolSite

Ligand :

HET Code:	ANP
Formula:	C10H13N6O12P3
Molecular weight:	502.164 g/mol
DrugBank ID:	-
Buried Surface Area:	43.42 %
Polar Surface area:	322.68 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-32.369	10.2416	-45.2154

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'	CG2	VAL- 212	4.45	0	Hydrophobic	false
N6	O	GLU- 274	2.77	173.8	H-Bond (Ligand Donor)	false
N1	N	VAL- 276	3.22	175.66	H-Bond (Protein Donor)	false
C2'	CB	ASP- 280	4.21	0	Hydrophobic	false
O2'	OD2	ASP- 280	2.89	164.84	H-Bond (Ligand Donor)	false
O3'	O	ASP- 323	3.33	138.16	H-Bond (Ligand Donor)	false
N3B	OD1	ASN- 324	2.56	129.96	H-Bond (Ligand Donor)	false
C2'	CD2	LEU- 326	3.71	0	Hydrophobic	false