scPDB - 4xeo entry

Protein Data Bank Entry:

PDB ID : 4xeo

Resolution :1.380 Å

Experimental Method : X-ray

Deposition Date : 2014-12-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Alanine--tRNA ligase, cytoplasmic
ID:	SYAC_HUMAN
AC:	P49588
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	13.419
Number of residues:	38
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.091	864.000

% Hydrophobic	% Polar
31.25	68.75
According to VolSite

Ligand :

HET Code:	A5A
Formula:	C13H19N7O7S
Molecular weight:	417.398 g/mol
DrugBank ID:	DB03376
Buried Surface Area:	78.09 %
Polar Surface area:	229.86 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
43.3821	1.48	-34.0718

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
O	NH2	ARG- 77	3.02	128.13	H-Bond (Protein Donor)	false
O1S	NH2	ARG- 77	2.99	143.95	H-Bond (Protein Donor)	false
O1S	NH1	ARG- 77	2.91	148.68	H-Bond (Protein Donor)	false
N6	O	HIS- 95	2.97	136.65	H-Bond (Ligand Donor)	false
N1	N	HIS- 95	2.96	170.57	H-Bond (Protein Donor)	false
C1'	CE1	PHE- 98	3.77	0	Hydrophobic	false
DuAr	DuAr	PHE- 98	3.68	0	Aromatic Face/Face	false
C5'	CE	MET- 100	3.66	0	Hydrophobic	false
O1S	NE1	TRP- 176	3.05	141.62	H-Bond (Protein Donor)	false
O3'	OE1	GLU- 213	2.69	162.79	H-Bond (Ligand Donor)	false
O2'	O	ILE- 214	2.98	130.02	H-Bond (Ligand Donor)	false
CB	CB	ASN- 216	4.48	0	Hydrophobic	false
C5'	CB	ASN- 216	4.23	0	Hydrophobic	false
N3S	OD1	ASN- 216	3.11	147.35	H-Bond (Ligand Donor)	false
CB	CG2	VAL- 218	3.8	0	Hydrophobic	false
N	OD2	ASP- 239	2.75	140.13	H-Bond (Ligand Donor)	false
N	OD2	ASP- 239	2.75	0	Ionic (Ligand Cationic)	false
N	OD1	ASP- 239	3.58	0	Ionic (Ligand Cationic)	false
O2'	N	GLY- 243	2.98	145.27	H-Bond (Protein Donor)	false
C2'	CD	ARG- 246	4.27	0	Hydrophobic	false
N	O	HOH- 689	2.81	163.62	H-Bond (Ligand Donor)	false
N3	O	HOH- 695	2.98	143.56	H-Bond (Protein Donor)	false