scPDB - 2yqz entry

Protein Data Bank Entry:

PDB ID : 2yqz

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2007-04-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Uncharacterized protein
ID:	Q5SLS0_THET8
AC:	Q5SLS0
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	300852
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	17.695
Number of residues:	37
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.058	1211.625

% Hydrophobic	% Polar
37.33	62.67
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	69.5 %
Polar Surface area:	189.77 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
25.3959	-3.02493	65.6461

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
O	OH	TYR- 12	2.71	173.49	H-Bond (Protein Donor)	false
SD	CZ	TYR- 12	4.02	0	Hydrophobic	false
CE	CE1	TYR- 12	4.48	0	Hydrophobic	false
CG	CZ	TYR- 12	3.92	0	Hydrophobic	false
N	OE2	GLU- 45	2.97	127.9	H-Bond (Ligand Donor)	false
N	OE2	GLU- 45	2.97	0	Ionic (Ligand Cationic)	false
N	O	GLY- 47	2.67	162.39	H-Bond (Ligand Donor)	false
O	CZ	ARG- 52	3.77	0	Ionic (Protein Cationic)	false
OXT	CZ	ARG- 52	3.71	0	Ionic (Protein Cationic)	false
O	NE	ARG- 52	3.09	145.24	H-Bond (Protein Donor)	false
OXT	NH2	ARG- 52	2.92	171.97	H-Bond (Protein Donor)	false
O3'	OD2	ASP- 68	2.59	162.53	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 68	3.26	121.97	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 68	2.75	161.62	H-Bond (Ligand Donor)	false
N3	N	ALA- 69	3.26	149.94	H-Bond (Protein Donor)	false
SD	CE	MET- 73	4.3	0	Hydrophobic	false
C3'	CE	MET- 73	3.94	0	Hydrophobic	false
N6	OD1	ASP- 94	3.09	171.75	H-Bond (Ligand Donor)	false
N6	OD2	ASP- 94	3.48	122.42	H-Bond (Ligand Donor)	false
N1	N	ALA- 95	2.88	165.6	H-Bond (Protein Donor)	false
N	O	VAL- 111	2.95	162.07	H-Bond (Ligand Donor)	false
CG	CB	HIS- 112	4.15	0	Hydrophobic	false
CE	CB	HIS- 112	3.83	0	Hydrophobic	false
C1'	CD1	LEU- 113	4.16	0	Hydrophobic	false
CE	CD1	LEU- 116	3.9	0	Hydrophobic	false
C5'	CD1	LEU- 116	3.56	0	Hydrophobic	false
O	O	HOH- 309	2.72	179.99	H-Bond (Protein Donor)	false