scPDB - 1gky entry

Protein Data Bank Entry:

PDB ID : 1gky

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 1991-12-23

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_YEAST
AC:	P15454
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	2.7.4.8

Chains:

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

Ligand binding site composition:

B-Factor:	17.323
Number of residues:	33
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.786	644.625

% Hydrophobic	% Polar
53.93	46.07
According to VolSite

Ligand :

HET Code:	5GP
Formula:	C10H12N5O8P
Molecular weight:	361.205 g/mol
DrugBank ID:	-
Buried Surface Area:	60.24 %
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
27.9455	40.1744	71.0162

Binding mode :

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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
O6	OG	SER- 34	2.69	160.18	H-Bond (Protein Donor)	false
O1P	CZ	ARG- 38	3.7	0	Ionic (Protein Cationic)	false
O2P	CZ	ARG- 38	3.88	0	Ionic (Protein Cationic)	false
O1P	NE	ARG- 38	2.84	151.5	H-Bond (Protein Donor)	false
O2P	NH2	ARG- 38	2.95	166.66	H-Bond (Protein Donor)	false
O3P	NH1	ARG- 41	3.22	148.16	H-Bond (Protein Donor)	false
O2P	OH	TYR- 50	2.61	144.89	H-Bond (Protein Donor)	false
N1	OE2	GLU- 69	2.86	143.76	H-Bond (Ligand Donor)	false
N1	OE1	GLU- 69	3.39	139.36	H-Bond (Ligand Donor)	false
N2	OE1	GLU- 69	2.82	170.99	H-Bond (Ligand Donor)	false
C5'	CD2	PHE- 73	3.78	0	Hydrophobic	false
O1P	OH	TYR- 78	2.76	139.55	H-Bond (Protein Donor)	false
C5'	CZ	TYR- 78	3.8	0	Hydrophobic	false
C1'	CD2	TYR- 78	4.44	0	Hydrophobic	false
C1'	CB	ASP- 100	4.43	0	Hydrophobic	false
N2	OD1	ASP- 100	2.89	159.82	H-Bond (Ligand Donor)	false
N3	N	ASP- 100	3.34	164.86	H-Bond (Protein Donor)	false
O2'	O	HOH- 260	3.27	179.97	H-Bond (Protein Donor)	false