scPDB - 3cfo entry

Protein Data Bank Entry:

PDB ID : 3cfo

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2008-03-04

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:	57.115
Number of residues:	28
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.326	273.375

% Hydrophobic	% Polar
55.56	44.44
According to VolSite

Ligand :

HET Code:	GMP
Formula:	C10H13N5O5
Molecular weight:	283.241 g/mol
DrugBank ID:	DB02857
Buried Surface Area:	69.53 %
Polar Surface area:	155.22 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	5
Rings:	3
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
7.7023	7.10565	55.6009

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
C4'	CB	SER- 36	3.97	0	Hydrophobic	false
C1'	CB	SER- 36	3.79	0	Hydrophobic	false
C5'	CZ	PHE- 38	4.46	0	Hydrophobic	false
C1'	CE2	PHE- 38	4.49	0	Hydrophobic	false
C5'	CD	ARG- 59	4.23	0	Hydrophobic	false
N7	N	MET- 85	3.05	157.76	H-Bond (Protein Donor)	false
O3'	OD1	ASP- 95	3.06	153.18	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 95	2.79	138.59	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 95	2.58	167.8	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 95	3.26	127.66	H-Bond (Ligand Donor)	false
C2'	CZ	PHE- 370	4.41	0	Hydrophobic	false
C2'	CD	LYS- 374	4.33	0	Hydrophobic	false
N1	O	LYS- 378	2.81	157.41	H-Bond (Ligand Donor)	false
N2	O	LYS- 378	3.19	137.38	H-Bond (Ligand Donor)	false
O6	N	ILE- 380	2.95	169.93	H-Bond (Protein Donor)	false