scPDB - 2f3r entry

Protein Data Bank Entry:

PDB ID : 2f3r

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2005-11-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Guanylate kinase
ID:	KGUA_ECOLI
AC:	P60546
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	2.7.4.8

Chains:

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

Ligand binding site composition:

B-Factor:	48.951
Number of residues:	49
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.139	759.375

% Hydrophobic	% Polar
28.00	72.00
According to VolSite

Ligand :

HET Code:	G5P
Formula:	C20H24N10O23P5
Molecular weight:	927.327 g/mol
DrugBank ID:	-
Buried Surface Area:	51.84 %
Polar Surface area:	559.37 Å2

Number of
H-Bond Acceptors:	30
H-Bond Donors:	7
Rings:	6
Aromatic rings:	3
Anionic atoms:	5
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	16

Mass center Coordinates

X	Y	Z
7.63843	17.3363	39.4905

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
O2G	OG	SER- 13	3.34	155.98	H-Bond (Protein Donor)	false
O2D	N	GLY- 14	3.12	133.79	H-Bond (Protein Donor)	false
O2D	N	GLY- 16	3.13	142.15	H-Bond (Protein Donor)	false
O1D	NZ	LYS- 17	3.4	178.05	H-Bond (Protein Donor)	false
O1D	NZ	LYS- 17	3.4	0	Ionic (Protein Cationic)	false
O1B	NZ	LYS- 17	3.35	0	Ionic (Protein Cationic)	false
O1D	N	SER- 18	2.76	166.58	H-Bond (Protein Donor)	false
O1D	OG	SER- 18	3.47	156.41	H-Bond (Protein Donor)	false
O3D	OG	SER- 18	2.77	134.04	H-Bond (Protein Donor)	false
O1E	N	SER- 19	3.38	142.97	H-Bond (Protein Donor)	false
O2E	OG	SER- 19	2.63	159.53	H-Bond (Protein Donor)	false
O6	OG	SER- 38	2.65	148.66	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 42	3.72	0	Ionic (Protein Cationic)	false
O2A	CZ	ARG- 42	3.55	0	Ionic (Protein Cationic)	false
O1A	NH2	ARG- 42	3.12	155.56	H-Bond (Protein Donor)	false
O1A	NE	ARG- 42	3.43	141.77	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 45	3.45	0	Ionic (Protein Cationic)	false
O1A	OH	TYR- 54	2.7	138.32	H-Bond (Protein Donor)	false
N1	OE1	GLU- 73	3.08	143.98	H-Bond (Ligand Donor)	false
N1	OE2	GLU- 73	3.15	145.41	H-Bond (Ligand Donor)	false
N2	OE1	GLU- 73	2.97	148.7	H-Bond (Ligand Donor)	false
C4'	CG1	VAL- 77	4.17	0	Hydrophobic	false
C1'	CG2	VAL- 77	4.21	0	Hydrophobic	false
N2	OD1	ASP- 104	2.77	160.72	H-Bond (Ligand Donor)	false
N3	N	ASP- 104	3.17	165.15	H-Bond (Protein Donor)	false
C1'	CB	ASP- 104	4.17	0	Hydrophobic	false
O2F	O	ARG- 134	2.81	161.97	H-Bond (Ligand Donor)	false
O1D	O	HOH- 609	2.76	142.04	H-Bond (Protein Donor)	false
O2'	O	HOH- 610	2.81	179.96	H-Bond (Protein Donor)	false