scPDB - 4i9q entry

Protein Data Bank Entry:

PDB ID : 4i9q

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2012-12-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	DNA-directed DNA polymerase
ID:	DPOL_BPR69
AC:	Q38087
Organism:	Enterobacteria phage RB69
Reign:	Viruses
TaxID:	12353
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	36.221
Number of residues:	28
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.266	293.625

% Hydrophobic	% Polar
47.13	52.87
According to VolSite

Ligand :

HET Code:	XG4
Formula:	C10H13N6O12P3
Molecular weight:	502.164 g/mol
DrugBank ID:	-
Buried Surface Area:	52.36 %
Polar Surface area:	318.13 Å2

Number of
H-Bond Acceptors:	15
H-Bond Donors:	4
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
-15.4736	7.27419	-29.0138

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
C1'	CB	SER- 36	3.73	0	Hydrophobic	false
C4'	CB	SER- 36	4.15	0	Hydrophobic	false
C1'	CE1	PHE- 38	3.84	0	Hydrophobic	false
C4'	CZ	PHE- 38	4.31	0	Hydrophobic	false
O1A	NZ	LYS- 48	3.34	133.37	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 48	3.34	0	Ionic (Protein Cationic)	false
O1B	NZ	LYS- 48	3.66	0	Ionic (Protein Cationic)	false
C5'	CZ	TYR- 49	3.62	0	Hydrophobic	false
O1G	CZ	ARG- 59	3.21	0	Ionic (Protein Cationic)	false
C4'	CD	ARG- 59	3.35	0	Hydrophobic	false
N7	N	MET- 85	3.36	166.73	H-Bond (Protein Donor)	false
N1	O	LYS- 378	2.91	150.89	H-Bond (Ligand Donor)	false
N2	O	LYS- 378	3.05	141.66	H-Bond (Ligand Donor)	false
O6	N	ILE- 380	3.33	169.32	H-Bond (Protein Donor)	false