scPDB - 1xqp entry

Protein Data Bank Entry:

PDB ID : 1xqp

Resolution :1.690 Å

Experimental Method : X-ray

Deposition Date : 2004-10-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	N-glycosylase/DNA lyase
ID:	AGOG_PYRAE
AC:	Q8ZVK6
Organism:	Pyrobaculum aerophilum
Reign:	Archaea
TaxID:	178306
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	31.628
Number of residues:	30
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.553	445.500

% Hydrophobic	% Polar
43.18	56.82
According to VolSite

Ligand :

HET Code:	8HG
Formula:	C10H13N5O5
Molecular weight:	283.241 g/mol
DrugBank ID:	DB02502
Buried Surface Area:	76.86 %
Polar Surface area:	149.51 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	5
Rings:	3
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
9.01345	25.4179	28.6371

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
O6	NE2	GLN- 31	2.87	164.07	H-Bond (Protein Donor)	false
N7	OE1	GLN- 31	2.68	166.06	H-Bond (Ligand Donor)	false
C1'	CB	SER- 58	4.41	0	Hydrophobic	false
O3'	O	SER- 58	2.66	160.65	H-Bond (Ligand Donor)	false
O20	NE1	TRP- 69	3.08	143.77	H-Bond (Protein Donor)	false
C3'	CD	LYS- 140	4.27	0	Hydrophobic	false
C5'	CB	LYS- 140	3.71	0	Hydrophobic	false
C1'	CE2	PHE- 144	4.31	0	Hydrophobic	false
C4'	CD2	PHE- 144	4.25	0	Hydrophobic	false
C5'	CB	PHE- 144	4.01	0	Hydrophobic	false
N2	O	PRO- 170	3.22	123.21	H-Bond (Ligand Donor)	false
C5'	CB	PRO- 170	4.4	0	Hydrophobic	false
C5'	CB	ASP- 172	4.38	0	Hydrophobic	false
C2'	CB	ASP- 172	3.71	0	Hydrophobic	false
N1	OD2	ASP- 218	2.8	150.16	H-Bond (Ligand Donor)	false
N2	OD1	ASP- 218	2.9	176	H-Bond (Ligand Donor)	false
C2'	CZ2	TRP- 222	4.16	0	Hydrophobic	false
O6	O	HOH- 272	2.88	179.97	H-Bond (Protein Donor)	false