scPDB - 4rd2 entry

Protein Data Bank Entry:

PDB ID : 4rd2

Resolution :1.580 Å

Experimental Method : X-ray

Deposition Date : 2014-09-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Translation initiation factor 2 subunit gamma
ID:	IF2G_SULSO
AC:	Q980A5
Organism:	Sulfolobus solfataricus
Reign:	Archaea
TaxID:	273057
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	33.528
Number of residues:	27
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.263	513.000

% Hydrophobic	% Polar
49.34	50.66
According to VolSite

Ligand :

HET Code:	GNP
Formula:	C10H13N6O13P3
Molecular weight:	518.164 g/mol
DrugBank ID:	DB02082
Buried Surface Area:	45.66 %
Polar Surface area:	338.36 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	5
Rings:	3
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-14.9022	-10.5174	37.2191

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
C5'	CD2	PHE- 221	4.25	0	Hydrophobic	false
C4'	CE1	PHE- 221	4.02	0	Hydrophobic	false
O1B	NZ	LYS- 225	2.95	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 225	3.27	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 225	3.27	154.84	H-Bond (Protein Donor)	false
C1'	CG1	VAL- 237	4.44	0	Hydrophobic	false
N1	OG	SER- 278	2.71	149.25	H-Bond (Ligand Donor)	false
N2	OG	SER- 278	2.83	141.47	H-Bond (Ligand Donor)	false
N2	O	SER- 278	3.36	128.53	H-Bond (Ligand Donor)	false
N2	O	ALA- 296	2.85	167.61	H-Bond (Ligand Donor)	false
C1'	CB	ALA- 296	3.62	0	Hydrophobic	false