scPDB - 3pd2 entry

Protein Data Bank Entry:

PDB ID : 3pd2

Resolution :1.860 Å

Experimental Method : X-ray

Deposition Date : 2010-10-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Threonine--tRNA ligase
ID:	SYT_PYRAB
AC:	Q9UZ14
Organism:	Pyrococcus abyssi
Reign:	Archaea
TaxID:	272844
EC Number:	6.1.1.3

Chains:

Chain Name:	Percentage of Residues within binding site
A	17 %
B	83 %

Ligand binding site composition:

B-Factor:	17.186
Number of residues:	36
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.935	415.125

% Hydrophobic	% Polar
50.41	49.59
According to VolSite

Ligand :

HET Code:	A3S
Formula:	C13H20N7O5
Molecular weight:	354.342 g/mol
DrugBank ID:	DB04024
Buried Surface Area:	74.4 %
Polar Surface area:	196.27 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	6
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
22.9023	-3.88432	4.37476

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
C4'	CB	ALA- 19	3.91	0	Hydrophobic	false
C4'	CD2	LEU- 20	4.48	0	Hydrophobic	false
N1	N	VAL- 45	3.03	165.11	H-Bond (Protein Donor)	false
N6	O	VAL- 45	2.77	161.09	H-Bond (Ligand Donor)	false
C2'	CB	PRO- 80	4.07	0	Hydrophobic	false
O	N	ALA- 82	2.91	164.69	H-Bond (Protein Donor)	false
C1'	CE1	PHE- 117	3.39	0	Hydrophobic	false
O2'	N	GLY- 118	2.93	158.02	H-Bond (Protein Donor)	false
N8	O	TYR- 119	3.05	161.27	H-Bond (Ligand Donor)	false
CB	CD1	TYR- 120	4.1	0	Hydrophobic	false
OG	N	LYS- 121	3.06	169.28	H-Bond (Protein Donor)	false
N	OE2	GLU- 134	3.67	0	Ionic (Ligand Cationic)	false
N	OE1	GLU- 134	2.75	0	Ionic (Ligand Cationic)	false
N	OE1	GLU- 134	2.75	169.45	H-Bond (Ligand Donor)	false