scPDB - 4dsj entry

Protein Data Bank Entry:

PDB ID : 4dsj

Resolution :2.860 Å

Experimental Method : X-ray

Deposition Date : 2012-02-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	DNA polymerase I
ID:	E1C9K5_GEOSE
AC:	E1C9K5
Organism:	Geobacillus stearothermophilus
Reign:	Bacteria
TaxID:	1422
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	64.469
Number of residues:	21
Including
Standard Amino Acids:	19
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:	CA CA

Cavity properties

Ligandability	Volume (Å3)
0.202	1181.250

% Hydrophobic	% Polar
26.29	73.71
According to VolSite

Ligand :

HET Code:	DGT
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB02181
Buried Surface Area:	35.13 %
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
31.4968	26.0574	65.6356

Binding mode :

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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
DuAr	CZ	ARG- 629	3.72	19.79	Pi/Cation	false
O1G	NH1	ARG- 702	2.86	158.19	H-Bond (Protein Donor)	false
O1G	CZ	ARG- 702	3.71	0	Ionic (Protein Cationic)	false
O1G	NZ	LYS- 706	3.3	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 706	3.25	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 706	3.25	169	H-Bond (Protein Donor)	false
DuAr	DuAr	PHE- 710	3.59	0	Aromatic Face/Face	false
C2'	CE1	PHE- 710	3.54	0	Hydrophobic	false
O2G	CA	CA- 1003	2.26	0	Metal Acceptor	false
O2B	CA	CA- 1003	2.42	0	Metal Acceptor	false