scPDB - 1zyd entry

Protein Data Bank Entry:

PDB ID : 1zyd

Resolution :2.750 Å

Experimental Method : X-ray

Deposition Date : 2005-06-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	eIF-2-alpha kinase GCN2
ID:	GCN2_YEAST
AC:	P15442
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	45.312
Number of residues:	33
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
0.534	371.250

% Hydrophobic	% Polar
58.18	41.82
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	51.59 %
Polar Surface area:	319.88 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
20.5333	27.7091	23.992

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
O1A	MG	MG- 307	2.1	0	Metal Acceptor	false
O3B	MG	MG- 308	2.42	0	Metal Acceptor	false
C4'	CB	LEU- 605	4.17	0	Hydrophobic	false
C1'	CB	LEU- 605	4.42	0	Hydrophobic	false
C5'	CG2	VAL- 613	3.32	0	Hydrophobic	false
C4'	CB	VAL- 613	3.95	0	Hydrophobic	false
C1'	CG1	VAL- 613	4.36	0	Hydrophobic	false
O1A	NZ	LYS- 628	3.77	0	Ionic (Protein Cationic)	false
N6	O	GLU- 789	3.05	163.56	H-Bond (Ligand Donor)	false
N1	N	CYS- 791	2.99	154.92	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 837	2.82	162.44	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 837	2.82	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 837	3.59	0	Ionic (Protein Cationic)	false
O3G	ND2	ASN- 840	3.26	158.09	H-Bond (Protein Donor)	false