scPDB - 3au2 entry

Protein Data Bank Entry:

PDB ID : 3au2

Resolution :1.400 Å

Experimental Method : X-ray

Deposition Date : 2011-01-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	DNA polymerase beta family (X family)
ID:	Q5SJ64_THET8
AC:	Q5SJ64
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	300852
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	13.611
Number of residues:	26
Including
Standard Amino Acids:	23
Non Standard Amino Acids:	2
Water Molecules:	1
Cofactors:
Metals:	CA CA

Cavity properties

Ligandability	Volume (Å3)
0.820	1255.500

% Hydrophobic	% Polar
38.44	61.56
According to VolSite

Ligand :

HET Code:	DGT
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB02181
Buried Surface Area:	50.73 %
Polar Surface area:	315.33 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	3
Rings:	3
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
15.7648	6.86084	-6.63358

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
O2G	NH1	ARG- 157	2.85	177.23	H-Bond (Protein Donor)	false
O3G	NH1	ARG- 157	3.48	120.13	H-Bond (Protein Donor)	false
O3G	NH2	ARG- 157	2.78	137.63	H-Bond (Protein Donor)	false
O2G	CZ	ARG- 157	3.68	0	Ionic (Protein Cationic)	false
O3G	CZ	ARG- 157	3.5	0	Ionic (Protein Cationic)	false
O3G	OG	SER- 188	2.59	171.92	H-Bond (Protein Donor)	false
O3B	OG	SER- 188	3.48	124.83	H-Bond (Protein Donor)	false
O2B	N	SER- 188	2.96	150.76	H-Bond (Protein Donor)	false
O1B	NH1	ARG- 191	3.07	176.87	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 191	3.92	0	Ionic (Protein Cationic)	false
O3G	N	GLY- 197	2.93	168.9	H-Bond (Protein Donor)	false
C4'	CD1	LEU- 259	4.25	0	Hydrophobic	false
O1G	CA	CA- 580	2.31	0	Metal Acceptor	false
O2B	CA	CA- 580	2.37	0	Metal Acceptor	false
O1A	CA	CA- 580	2.44	0	Metal Acceptor	false
O1A	CA	CA- 581	2.46	0	Metal Acceptor	false