scPDB - 4dfk entry

Protein Data Bank Entry:

PDB ID : 4dfk

Resolution :1.650 Å

Experimental Method : X-ray

Deposition Date : 2012-01-24

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:	33.939
Number of residues:	38
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	2
Water Molecules:	1
Cofactors:
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
0.251	1036.125

% Hydrophobic	% Polar
35.18	64.82
According to VolSite

Ligand :

HET Code:	0L5
Formula:	C24H36N3O16P3
Molecular weight:	715.474 g/mol
DrugBank ID:	-
Buried Surface Area:	52.6 %
Polar Surface area:	328.77 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	4
Rings:	2
Aromatic rings:	0
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	22

Mass center Coordinates

X	Y	Z
19.0698	-13.9733	-7.42276

Binding mode :

What is Poseview ?

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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
C39	CD	ARG- 587	4.24	0	Hydrophobic	false
O3B	N	GLN- 613	3.38	137.15	H-Bond (Protein Donor)	false
O1G	N	GLN- 613	2.94	157.83	H-Bond (Protein Donor)	false
O1B	N	ILE- 614	3.25	170.18	H-Bond (Protein Donor)	false
C4'	CG2	ILE- 614	3.93	0	Hydrophobic	false
O3'	N	GLU- 615	3.09	164.39	H-Bond (Protein Donor)	false
C2'	CG	GLU- 615	3.8	0	Hydrophobic	false
O2B	NE2	HIS- 639	3	163.44	H-Bond (Protein Donor)	false
C43	CZ	PHE- 647	3.94	0	Hydrophobic	false
C45	CE1	PHE- 647	3.78	0	Hydrophobic	false
C39	CD1	LEU- 657	3.8	0	Hydrophobic	false
C42	CG	LEU- 657	4.28	0	Hydrophobic	false
C44	CD2	LEU- 657	3.59	0	Hydrophobic	false
O1G	NH2	ARG- 659	3.05	166.87	H-Bond (Protein Donor)	false
O3G	NH1	ARG- 659	2.78	176.13	H-Bond (Protein Donor)	false
O1G	CZ	ARG- 659	3.9	0	Ionic (Protein Cationic)	false
O3G	CZ	ARG- 659	3.66	0	Ionic (Protein Cationic)	false
O36	NH1	ARG- 660	3.02	125.43	H-Bond (Protein Donor)	false
O36	NE	ARG- 660	2.88	130.83	H-Bond (Protein Donor)	false
C38	CB	ARG- 660	3.93	0	Hydrophobic	false
C32	CB	ARG- 660	4.13	0	Hydrophobic	false
C40	CB	ALA- 661	3.86	0	Hydrophobic	false
C41	CB	ALA- 661	3.52	0	Hydrophobic	false
C32	CB	LYS- 663	4.24	0	Hydrophobic	false
O1A	NZ	LYS- 663	2.77	164.02	H-Bond (Protein Donor)	false
O3G	NZ	LYS- 663	2.83	162.47	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 663	2.77	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 663	2.83	0	Ionic (Protein Cationic)	false
N34	OG1	THR- 664	2.81	143.5	H-Bond (Ligand Donor)	false
C2'	CZ	PHE- 667	3.38	0	Hydrophobic	false
C5'	CB	ASP- 785	4.23	0	Hydrophobic	false
O2A	MG	MG- 902	2.07	0	Metal Acceptor	false
O1B	MG	MG- 902	2.03	0	Metal Acceptor	false
O2G	MG	MG- 902	2.05	0	Metal Acceptor	false
O2A	MG	MG- 903	2.46	0	Metal Acceptor	false