scPDB - 3zxs entry

Protein Data Bank Entry:

PDB ID : 3zxs

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2011-08-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Deoxyribodipyrimidine photolyase-related protein
ID:	Q3IXP1_RHOS4
AC:	Q3IXP1
Organism:	Rhodobacter sphaeroides
Reign:	Bacteria
TaxID:	272943
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	27.465
Number of residues:	34
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.983	330.750

% Hydrophobic	% Polar
63.27	36.73
According to VolSite

Ligand :

HET Code:	DLZ
Formula:	C13H18N4O6
Molecular weight:	326.305 g/mol
DrugBank ID:	-
Buried Surface Area:	74.98 %
Polar Surface area:	155.04 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	5
Rings:	2
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
3.33848	17.3784	301.557

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	N	GLY- 9	3.13	138	H-Bond (Protein Donor)	false
N1	N	GLY- 9	3.33	143.65	H-Bond (Protein Donor)	false
O5'	OD2	ASP- 10	2.82	178.14	H-Bond (Ligand Donor)	false
N3	O	ALA- 32	2.8	175.84	H-Bond (Ligand Donor)	false
O4	N	VAL- 34	3.14	155.64	H-Bond (Protein Donor)	false
C2'	CG	GLU- 37	4.5	0	Hydrophobic	false
O2'	OE1	GLU- 37	2.96	156.39	H-Bond (Ligand Donor)	false
C6	CG1	ILE- 48	4.34	0	Hydrophobic	false
C7	CG1	ILE- 51	4.35	0	Hydrophobic	false
C6	CD1	ILE- 51	4.24	0	Hydrophobic	false
C1'	CD1	ILE- 51	4.04	0	Hydrophobic	false
O5'	N	GLY- 105	3.13	164.37	H-Bond (Protein Donor)	false
C5'	CB	ASP- 106	3.91	0	Hydrophobic	false
C7	CD2	LEU- 395	4.26	0	Hydrophobic	false
C1'	CD2	LEU- 395	4.42	0	Hydrophobic	false
C5'	CD2	LEU- 395	4.13	0	Hydrophobic	false