scPDB - 5ah5 entry

Protein Data Bank Entry:

PDB ID : 5ah5

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2015-02-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Leucine--tRNA ligase
ID:	B9JQP8_AGRRK
AC:	B9JQP8
Organism:	Agrobacterium radiobacter
Reign:	Bacteria
TaxID:	311403
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	31.828
Number of residues:	38
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.764	1181.250

% Hydrophobic	% Polar
31.43	68.57
According to VolSite

Ligand :

HET Code:	LSS
Formula:	C16H25N7O7S
Molecular weight:	459.477 g/mol
DrugBank ID:	-
Buried Surface Area:	74.17 %
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:	8

Mass center Coordinates

X	Y	Z
19.4805	-1.10768	2.43216

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
C23	CB	MET- 38	4.02	0	Hydrophobic	false
C11	CB	MET- 38	3.73	0	Hydrophobic	false
N4	O	PHE- 39	2.88	158.1	H-Bond (Ligand Donor)	false
C7	CE1	PHE- 39	3.81	0	Hydrophobic	false
C9	CD1	PHE- 39	4.49	0	Hydrophobic	false
C11	CD1	PHE- 39	3.79	0	Hydrophobic	false
O2A	N	TYR- 41	3.35	143.36	H-Bond (Protein Donor)	false
N7	NE2	HIS- 47	2.84	168.75	H-Bond (Protein Donor)	false
O2A	NE2	HIS- 50	2.82	161.83	H-Bond (Protein Donor)	false
O3	OD1	ASN- 53	2.52	158.93	H-Bond (Ligand Donor)	false
C21	CB	ASN- 53	4.38	0	Hydrophobic	false
N4	OD2	ASP- 78	2.71	154.53	H-Bond (Ligand Donor)	false
N4	OD2	ASP- 78	2.71	0	Ionic (Ligand Cationic)	false
C10	CE1	PHE- 490	4.14	0	Hydrophobic	false
C10	CB	SER- 493	3.71	0	Hydrophobic	false
C11	CE1	TYR- 496	4.11	0	Hydrophobic	false
O3	N	GLY- 526	3.2	138.7	H-Bond (Protein Donor)	false
O1	NE2	HIS- 529	2.79	162.57	H-Bond (Protein Donor)	false
C10	CB	HIS- 533	3.58	0	Hydrophobic	false
C11	CB	HIS- 533	4.49	0	Hydrophobic	false
O2	NE2	GLN- 562	3.32	129.85	H-Bond (Protein Donor)	false
N3	NE2	GLN- 562	3.01	160.99	H-Bond (Protein Donor)	false
N1	N	VAL- 565	2.87	174.62	H-Bond (Protein Donor)	false
N6	O	VAL- 565	3.23	173.07	H-Bond (Ligand Donor)	false