scPDB - 3kt3 entry

Protein Data Bank Entry:

PDB ID : 3kt3

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2009-11-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Tryptophan--tRNA ligase, cytoplasmic
ID:	SYWC_YEAST
AC:	Q12109
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	6.1.1.2

Chains:

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

Ligand binding site composition:

B-Factor:	40.311
Number of residues:	45
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.060	779.625

% Hydrophobic	% Polar
34.63	65.37
According to VolSite

Ligand :

HET Code:	TYM
Formula:	C21H24N7O8P
Molecular weight:	533.431 g/mol
DrugBank ID:	DB01831
Buried Surface Area:	82.42 %
Polar Surface area:	248.2 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	5
Rings:	5
Aromatic rings:	4
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
-153.863	26.9954	-25.813

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
NE1	OH	TYR- 106	2.97	158.01	H-Bond (Ligand Donor)	false
CH2	CB	THR- 107	4.5	0	Hydrophobic	false
O1P	NH1	ARG- 109	2.94	143.49	H-Bond (Protein Donor)	false
O1P	CZ	ARG- 109	3.88	0	Ionic (Protein Cationic)	false
C5'	CD	ARG- 109	4.29	0	Hydrophobic	false
O1P	N	GLY- 110	2.67	167.69	H-Bond (Protein Donor)	false
C1'	CG	PRO- 123	3.77	0	Hydrophobic	false
C4'	CG	PRO- 123	3.92	0	Hydrophobic	false
NE1	OE1	GLU- 141	3.16	121.55	H-Bond (Ligand Donor)	false
CB	CG2	THR- 143	4.13	0	Hydrophobic	false
NH3	OE2	GLU- 146	3.23	0	Ionic (Ligand Cationic)	false
NH3	OE1	GLU- 146	2.68	0	Ionic (Ligand Cationic)	false
NH3	OE1	GLU- 146	2.68	141.85	H-Bond (Ligand Donor)	false
O	NZ	LYS- 147	3.49	147.25	H-Bond (Protein Donor)	false
NH3	OE1	GLN- 230	2.94	165.16	H-Bond (Ligand Donor)	false
CE2	CG	GLN- 230	4.24	0	Hydrophobic	false
CH2	CG2	ILE- 253	3.77	0	Hydrophobic	false
CZ3	CB	CYS- 255	3.61	0	Hydrophobic	false
O2'	N	ALA- 256	3.02	137.97	H-Bond (Protein Donor)	false
C1'	CB	ALA- 256	4	0	Hydrophobic	false
O2'	OD1	ASP- 258	2.59	153.38	H-Bond (Ligand Donor)	false
C3'	CG	GLN- 259	4.02	0	Hydrophobic	false
CE3	CG	GLN- 259	3.75	0	Hydrophobic	false
CZ2	CZ	PHE- 263	3.46	0	Hydrophobic	false
N1	N	PHE- 286	2.83	159.47	H-Bond (Protein Donor)	false
N6	O	PHE- 286	3.13	173.27	H-Bond (Ligand Donor)	false
N6	O	MET- 296	3.15	150.99	H-Bond (Ligand Donor)	false
O3'	O	HOH- 464	2.74	156.32	H-Bond (Ligand Donor)	false