scPDB - 1lvg entry

Protein Data Bank Entry:

PDB ID : 1lvg

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2002-05-28

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_MOUSE
AC:	Q64520
Organism:	Mus musculus
Reign:	Eukaryota
TaxID:	10090
EC Number:	2.7.4.8

Chains:

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

Ligand binding site composition:

B-Factor:	23.019
Number of residues:	42
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	2
Water Molecules:	3
Cofactors:	ADP
Metals:	K

Cavity properties

Ligandability	Volume (Å3)
0.608	924.750

% Hydrophobic	% Polar
41.24	58.76
According to VolSite

Ligand :

HET Code:	5GP
Formula:	C10H12N5O8P
Molecular weight:	361.205 g/mol
DrugBank ID:	-
Buried Surface Area:	77.02 %
Polar Surface area:	217.22 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
87.8628	-29.9886	46.8682

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
O6	OG	SER- 37	2.57	167.78	H-Bond (Protein Donor)	false
O1P	NE	ARG- 41	2.72	163.09	H-Bond (Protein Donor)	false
O2P	NH2	ARG- 41	2.9	159.32	H-Bond (Protein Donor)	false
O1P	CZ	ARG- 41	3.69	0	Ionic (Protein Cationic)	false
O2P	CZ	ARG- 41	3.63	0	Ionic (Protein Cationic)	false
O3P	CZ	ARG- 44	3.69	0	Ionic (Protein Cationic)	false
O3P	NH2	ARG- 44	2.81	149.45	H-Bond (Protein Donor)	false
O2P	OH	TYR- 53	2.56	139.69	H-Bond (Protein Donor)	false
N1	OE2	GLU- 72	2.77	157	H-Bond (Ligand Donor)	false
N1	OE1	GLU- 72	3.46	139.57	H-Bond (Ligand Donor)	false
N2	OE1	GLU- 72	2.87	175.71	H-Bond (Ligand Donor)	false
C4'	CD2	PHE- 76	3.49	0	Hydrophobic	false
O1P	OH	TYR- 81	2.57	142.82	H-Bond (Protein Donor)	false
C1'	CD2	TYR- 81	4.4	0	Hydrophobic	false
C5'	CZ	TYR- 81	3.72	0	Hydrophobic	false
O2'	OD2	ASP- 101	2.62	161.77	H-Bond (Ligand Donor)	false
C1'	CB	ASP- 103	4.14	0	Hydrophobic	false
N2	OD1	ASP- 103	2.82	165.94	H-Bond (Ligand Donor)	false
N3	N	ASP- 103	3.01	161.98	H-Bond (Protein Donor)	false
O1P	CZ	ARG- 148	3.72	0	Ionic (Protein Cationic)	false
O3P	CZ	ARG- 148	3.77	0	Ionic (Protein Cationic)	false
O1P	NH2	ARG- 148	2.87	168.27	H-Bond (Protein Donor)	false
O3P	NH1	ARG- 148	2.93	167.72	H-Bond (Protein Donor)	false