scPDB - 2aly entry

Protein Data Bank Entry:

PDB ID : 2aly

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2005-08-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Phenylalanine--tRNA ligase alpha subunit
ID:	SYFA_THETH
AC:	P27001
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	274
EC Number:	6.1.1.20

Chains:

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

Ligand binding site composition:

B-Factor:	33.984
Number of residues:	44
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.000	668.250

% Hydrophobic	% Polar
37.88	62.12
According to VolSite

Ligand :

HET Code:	YSA
Formula:	C19H23N7O8S
Molecular weight:	509.493 g/mol
DrugBank ID:	DB03325
Buried Surface Area:	74.06 %
Polar Surface area:	250.09 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	5
Rings:	4
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
15.3555	62.6922	17.0251

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
N	ND1	HIS- 178	3.02	153.83	H-Bond (Ligand Donor)	false
O	NH2	ARG- 204	2.8	122.61	H-Bond (Protein Donor)	false
OAD	NH2	ARG- 204	2.68	136.28	H-Bond (Protein Donor)	false
OAD	NH1	ARG- 204	2.72	134.27	H-Bond (Protein Donor)	false
O5'	NH2	ARG- 204	3.47	141.61	H-Bond (Protein Donor)	false
N6	OE1	GLU- 206	3.2	146.05	H-Bond (Ligand Donor)	false
N1	N	GLU- 213	2.85	171.01	H-Bond (Protein Donor)	false
N6	O	GLU- 213	2.68	127.74	H-Bond (Ligand Donor)	false
C1'	CE2	PHE- 216	4.19	0	Hydrophobic	false
DuAr	DuAr	PHE- 216	3.4	0	Aromatic Face/Face	false
O4'	NE2	GLN- 218	3.22	163.15	H-Bond (Protein Donor)	false
N	OE2	GLU- 220	3.94	0	Ionic (Ligand Cationic)	false
CB	CE1	PHE- 258	3.68	0	Hydrophobic	false
CD1	CE2	PHE- 258	3.38	0	Hydrophobic	false
CE1	CB	PHE- 258	4.41	0	Hydrophobic	false
CB	CE2	PHE- 260	4.42	0	Hydrophobic	false
CE1	CG2	VAL- 261	4.06	0	Hydrophobic	false
CZ	CG1	VAL- 261	4.38	0	Hydrophobic	false
CZ	CB	ALA- 314	4.3	0	Hydrophobic	false
N	O	HOH- 1002	2.74	161.36	H-Bond (Ligand Donor)	false
N7	O	HOH- 1025	2.62	167.67	H-Bond (Protein Donor)	false