scPDB - 4df8 entry

Protein Data Bank Entry:

PDB ID : 4df8

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2012-01-23

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, thermostable
ID:	DPO1_THEAQ
AC:	P19821
Organism:	Thermus aquaticus
Reign:	Bacteria
TaxID:	271
EC Number:	2.7.7.7

Chains:

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

Ligand binding site composition:

B-Factor:	29.575
Number of residues:	33
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	3
Water Molecules:	1
Cofactors:
Metals:	CL MG MG

Cavity properties

Ligandability	Volume (Å3)
0.274	1039.500

% Hydrophobic	% Polar
38.64	61.36
According to VolSite

Ligand :

HET Code:	0L4
Formula:	C16H21N5O12P3
Molecular weight:	568.286 g/mol
DrugBank ID:	-
Buried Surface Area:	55.83 %
Polar Surface area:	314.4 Å2

Number of
H-Bond Acceptors:	15
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
18.6533	-17.5121	-9.06186

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
O1G	N	GLN- 613	2.84	154.46	H-Bond (Protein Donor)	false
O2B	N	ILE- 614	3.39	168.7	H-Bond (Protein Donor)	false
C4'	CG2	ILE- 614	3.84	0	Hydrophobic	false
O3'	N	GLU- 615	3.03	161.5	H-Bond (Protein Donor)	false
C2'	CG	GLU- 615	3.68	0	Hydrophobic	false
O1B	NE2	HIS- 639	3.04	163.85	H-Bond (Protein Donor)	false
O3T	CZ	ARG- 659	3.73	0	Ionic (Protein Cationic)	false
O1G	CZ	ARG- 659	3.88	0	Ionic (Protein Cationic)	false
O3T	NH1	ARG- 659	2.88	174.34	H-Bond (Protein Donor)	false
O1G	NH2	ARG- 659	2.98	168.29	H-Bond (Protein Donor)	false
C45	CG	ARG- 660	3.91	0	Hydrophobic	false
O2A	NZ	LYS- 663	3.85	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 663	2.75	0	Ionic (Protein Cationic)	false
O3T	NZ	LYS- 663	2.68	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 663	2.75	161.1	H-Bond (Protein Donor)	false
O3A	NZ	LYS- 663	3.47	125.72	H-Bond (Protein Donor)	false
O3T	NZ	LYS- 663	2.68	156.92	H-Bond (Protein Donor)	false
C44	CB	LYS- 663	4.26	0	Hydrophobic	false
C43	CB	LYS- 663	4.18	0	Hydrophobic	false
C44	CG2	THR- 664	3.85	0	Hydrophobic	false
C2'	CE2	PHE- 667	3.52	0	Hydrophobic	false
C3'	CZ	PHE- 667	3.5	0	Hydrophobic	false
C5	CB	PHE- 667	4.18	0	Hydrophobic	false
C5'	CB	ASP- 785	4.21	0	Hydrophobic	false
O2A	MG	MG- 902	2.48	0	Metal Acceptor	false
O2A	MG	MG- 903	2.08	0	Metal Acceptor	false
O2G	MG	MG- 903	2.17	0	Metal Acceptor	false
O2B	MG	MG- 903	2.1	0	Metal Acceptor	false
N3	O	HOH- 1007	3.08	179.98	H-Bond (Protein Donor)	false