scPDB - 1wyg entry

Protein Data Bank Entry:

PDB ID : 1wyg

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2005-02-14

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
A	100 %

Ligand binding site composition:

B-Factor:	36.331
Number of residues:	60
Including
Standard Amino Acids:	58
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.025	1576.125

% Hydrophobic	% Polar
42.83	57.17
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	72.45 %
Polar Surface area:	381.7 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	7
Rings:	6
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
-9.62868	95.5017	30.1853

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
C8M	CD1	LEU- 74	4.13	0	Hydrophobic	false
C3B	CD	LYS- 255	4.1	0	Hydrophobic	false
O2B	N	LEU- 256	3.47	121.88	H-Bond (Protein Donor)	false
O2B	O	LEU- 256	3.22	131.18	H-Bond (Ligand Donor)	false
C2B	CB	LEU- 256	3.78	0	Hydrophobic	false
O1A	N	VAL- 258	2.79	168.38	H-Bond (Protein Donor)	false
O1P	N	GLY- 259	3.17	156.07	H-Bond (Protein Donor)	false
O1A	N	ASN- 260	2.96	145.4	H-Bond (Protein Donor)	false
C8M	CB	THR- 261	4.45	0	Hydrophobic	false
C2'	CB	THR- 261	4.36	0	Hydrophobic	false
O2'	OG1	THR- 261	2.88	161.15	H-Bond (Ligand Donor)	false
O2P	N	THR- 261	3.02	133.71	H-Bond (Protein Donor)	false
O2A	N	GLU- 262	2.81	137.34	H-Bond (Protein Donor)	false
C5B	CB	GLU- 262	3.69	0	Hydrophobic	false
C5'	CB	GLU- 262	4.16	0	Hydrophobic	false
O2A	N	ILE- 263	2.82	165.73	H-Bond (Protein Donor)	false
C3B	CD1	ILE- 263	3.66	0	Hydrophobic	false
C5B	CG1	ILE- 263	4.09	0	Hydrophobic	false
C8M	CG1	ILE- 265	4.33	0	Hydrophobic	false
C3'	CZ	PHE- 336	4.15	0	Hydrophobic	false
C6	CB	ALA- 337	3.66	0	Hydrophobic	false
C9	CG1	VAL- 341	4.34	0	Hydrophobic	false
C7	CG2	VAL- 341	4.07	0	Hydrophobic	false
C4'	CB	ALA- 345	3.68	0	Hydrophobic	false
O4'	O	SER- 346	2.91	146.53	H-Bond (Ligand Donor)	false
O5'	N	SER- 346	3.4	128.39	H-Bond (Protein Donor)	false
O1P	OG	SER- 346	2.77	176.47	H-Bond (Protein Donor)	false
O1P	N	SER- 346	2.87	168.66	H-Bond (Protein Donor)	false
O2	ND2	ASN- 350	2.77	146.76	H-Bond (Protein Donor)	false
C4'	CB	ASN- 350	4.23	0	Hydrophobic	false
C1B	CB	ILE- 352	3.9	0	Hydrophobic	false
O2	N	ASP- 359	3.26	158.85	H-Bond (Protein Donor)	false
N6A	O	LEU- 403	2.96	139.94	H-Bond (Ligand Donor)	false
N1A	N	LEU- 403	2.8	136.44	H-Bond (Protein Donor)	false