scPDB - 3kfl entry

Protein Data Bank Entry:

PDB ID : 3kfl

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2009-10-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative methionyl-tRNA synthetase
ID:	Q4QCD2_LEIMA
AC:	Q4QCD2
Organism:	Leishmania major
Reign:	Eukaryota
TaxID:	5664
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	29.598
Number of residues:	43
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.075	286.875

% Hydrophobic	% Polar
54.12	45.88
According to VolSite

Ligand :

HET Code:	ME8
Formula:	C15H23N6O8PS
Molecular weight:	478.417 g/mol
DrugBank ID:	-
Buried Surface Area:	86.73 %
Polar Surface area:	257.71 Å2

Number of
H-Bond Acceptors:	13
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
33.31	44.7912	-5.10697

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
CB	CB	PRO- 216	4.15	0	Hydrophobic	false
SD	CB	PRO- 216	3.92	0	Hydrophobic	false
C4'	CG	PRO- 216	4.33	0	Hydrophobic	false
N2	O	ILE- 217	2.62	172.3	H-Bond (Ligand Donor)	false
SD	CG1	ILE- 217	3.78	0	Hydrophobic	false
C1'	CE1	TYR- 218	4.37	0	Hydrophobic	false
C4'	CE1	TYR- 218	4.17	0	Hydrophobic	false
O1	N	TYR- 219	3.35	153.82	H-Bond (Protein Donor)	false
O1S	N	TYR- 219	2.79	138.9	H-Bond (Protein Donor)	false
O2'	OG	SER- 231	2.66	167.81	H-Bond (Ligand Donor)	false
N2	OD2	ASP- 256	2.82	160.99	H-Bond (Ligand Donor)	false
N2	OD2	ASP- 256	2.82	0	Ionic (Ligand Cationic)	false
CB	CH2	TRP- 443	3.35	0	Hydrophobic	false
CG	CZ3	TRP- 443	3.28	0	Hydrophobic	false
CE	CB	ALA- 446	3.88	0	Hydrophobic	false
CG	CB	ALA- 446	4.29	0	Hydrophobic	false
CE	CD2	LEU- 447	4.2	0	Hydrophobic	false
CE	CZ	TYR- 450	3.97	0	Hydrophobic	false
O3'	N	GLY- 484	3.03	133.81	H-Bond (Protein Donor)	false
O3'	OD2	ASP- 486	2.66	154.04	H-Bond (Ligand Donor)	false
CB	CD1	ILE- 487	3.87	0	Hydrophobic	false
SD	CD1	ILE- 487	4.38	0	Hydrophobic	false
N1	N	TRP- 516	2.95	152.31	H-Bond (Protein Donor)	false
N6	O	TRP- 516	2.94	164.64	H-Bond (Ligand Donor)	false
N7	NZ	LYS- 522	3.09	159.48	H-Bond (Protein Donor)	false
N6	O	ILE- 523	2.85	164.89	H-Bond (Ligand Donor)	false
O1S	NZ	LYS- 525	2.63	171.81	H-Bond (Protein Donor)	false
O1S	NZ	LYS- 525	2.63	0	Ionic (Protein Cationic)	false
O2S	NZ	LYS- 525	3.82	0	Ionic (Protein Cationic)	false
O2S	MG	MG- 803	2.2	0	Metal Acceptor	false