scPDB - 4ytz entry

Protein Data Bank Entry:

PDB ID : 4ytz

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2015-03-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Xanthine dehydrogenase/oxidase
ID:	XDH_RAT
AC:	P22985
Organism:	Rattus norvegicus
Reign:	Eukaryota
TaxID:	10116
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	25.530
Number of residues:	26
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.417	580.500

% Hydrophobic	% Polar
69.19	30.81
According to VolSite

Ligand :

HET Code:	URC
Formula:	C5H4N4O3
Molecular weight:	168.110 g/mol
DrugBank ID:	DB08844
Buried Surface Area:	74.65 %
Polar Surface area:	99.32 Å2

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

Mass center Coordinates

X	Y	Z
10.9473	-11.7542	68.3634

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
O13	OE2	GLU- 802	2.68	155.86	H-Bond (Protein Donor)	false
N7	OE1	GLU- 802	2.62	171.08	H-Bond (Ligand Donor)	false
O11	NH2	ARG- 880	2.8	155.16	H-Bond (Protein Donor)	false
O11	NE	ARG- 880	3.13	138.86	H-Bond (Protein Donor)	false
O11	N	THR- 1010	3.15	158.04	H-Bond (Protein Donor)	false
N9	OE2	GLU- 1261	2.84	162.24	H-Bond (Ligand Donor)	false