scPDB - 4xba entry

Protein Data Bank Entry:

PDB ID : 4xba

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 2014-12-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Aprataxin-like protein
ID:	APTX_SCHPO
AC:	O74859
Organism:	Schizosaccharomyces pombe
Reign:	Eukaryota
TaxID:	284812
EC Number:	3

Chains:

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

Ligand binding site composition:

B-Factor:	16.681
Number of residues:	30
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.682	506.250

% Hydrophobic	% Polar
56.67	43.33
According to VolSite

Ligand :

HET Code:	5GP
Formula:	C10H12N5O8P
Molecular weight:	361.205 g/mol
DrugBank ID:	-
Buried Surface Area:	69.59 %
Polar Surface area:	217.22 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
4.08058	12.95	8.42204

Binding mode :

What is Poseview ?

2D View
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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
N1	OH	TYR- 41	2.7	153.61	H-Bond (Ligand Donor)	false
N2	OH	TYR- 41	3	135.91	H-Bond (Ligand Donor)	false
N2	O	ARG- 62	3.01	135.86	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 63	2.58	172.52	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 63	3.45	125.27	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 63	2.65	167.01	H-Bond (Ligand Donor)	false
N3	N	MET- 64	3.22	168.47	H-Bond (Protein Donor)	false
C2'	CD2	PHE- 65	4.22	0	Hydrophobic	false
C4'	CD1	LEU- 73	4.43	0	Hydrophobic	false
C1'	CD1	LEU- 73	4.47	0	Hydrophobic	false
O2P	N	SER- 142	3.26	134.39	H-Bond (Protein Donor)	false
C5'	CG	MET- 143	3.68	0	Hydrophobic	false
O1P	NE2	HIS- 149	2.95	162.94	H-Bond (Protein Donor)	false
O1P	O	HOH- 461	2.89	147.3	H-Bond (Protein Donor)	false