scPDB - 4py2 entry

Protein Data Bank Entry:

PDB ID : 4py2

Resolution :2.150 Å

Experimental Method : X-ray

Deposition Date : 2014-03-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Methionine--tRNA ligase
ID:	Q2YQ76_BRUA2
AC:	Q2YQ76
Organism:	Brucella abortus
Reign:	Bacteria
TaxID:	359391
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	35.149
Number of residues:	38
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.145	732.375

% Hydrophobic	% Polar
50.69	49.31
According to VolSite

Ligand :

HET Code:	43E
Formula:	C15H18Cl2N3OS
Molecular weight:	359.294 g/mol
DrugBank ID:	-
Buried Surface Area:	66.31 %
Polar Surface area:	85.98 Å2

Number of
H-Bond Acceptors:	1
H-Bond Donors:	3
Rings:	2
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
-6.23509	16.5815	66.9571

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
CLC	CB	ALA- 11	3.83	0	Hydrophobic	false
CLC	CG1	ILE- 12	3.71	0	Hydrophobic	false
CAJ	CG	TYR- 14	3.59	0	Hydrophobic	false
NAO	OD2	ASP- 51	2.86	165.61	H-Bond (Ligand Donor)	false
NAP	OD1	ASP- 51	3.09	160.4	H-Bond (Ligand Donor)	false
NAP	OD2	ASP- 51	3.4	138.41	H-Bond (Ligand Donor)	false
CLB	CG2	VAL- 229	4.22	0	Hydrophobic	false
SAQ	CB	VAL- 229	4.43	0	Hydrophobic	false
CAH	CG2	VAL- 229	4.4	0	Hydrophobic	false
CLB	CE3	TRP- 230	3.5	0	Hydrophobic	false
CAG	CB	ALA- 233	3.78	0	Hydrophobic	false
CLB	CG	LEU- 234	4.19	0	Hydrophobic	false
CAG	CD2	LEU- 234	3.93	0	Hydrophobic	false
CLC	CZ	TYR- 237	4.04	0	Hydrophobic	false
CAU	CG2	ILE- 265	4	0	Hydrophobic	false
CAI	CD1	ILE- 265	3.81	0	Hydrophobic	false
CLB	CB	PHE- 268	3.77	0	Hydrophobic	false
NAN	O	HOH- 733	2.6	151.47	H-Bond (Ligand Donor)	false