scPDB - 2zw9 entry

Protein Data Bank Entry:

PDB ID : 2zw9

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2008-12-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	tRNA wybutosine-synthesizing protein 4
ID:	TYW4_YEAST
AC:	Q08282
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	2.1.1.290

Chains:

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

Ligand binding site composition:

B-Factor:	60.924
Number of residues:	39
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.213	448.875

% Hydrophobic	% Polar
39.85	60.15
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	81.67 %
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
32.6164	-15.3172	-22.164

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
C2'	CG2	ILE- 27	3.92	0	Hydrophobic	false
CE	CB	THR- 30	3.87	0	Hydrophobic	false
SD	CB	ASN- 31	4.18	0	Hydrophobic	false
C3'	CB	ASN- 31	4.3	0	Hydrophobic	false
CE	CB	SER- 34	4.42	0	Hydrophobic	false
O	NZ	LYS- 38	2.75	155.02	H-Bond (Protein Donor)	false
OXT	NZ	LYS- 38	3.25	138.79	H-Bond (Protein Donor)	false
O	NZ	LYS- 38	2.75	0	Ionic (Protein Cationic)	false
OXT	NZ	LYS- 38	3.25	0	Ionic (Protein Cationic)	false
O	NH1	ARG- 88	2.93	131.1	H-Bond (Protein Donor)	false
O	CZ	ARG- 88	3.91	0	Ionic (Protein Cationic)	false
O3'	OD2	ASP- 146	2.97	160.58	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 146	2.58	150.06	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 146	3.3	139.57	H-Bond (Ligand Donor)	false
DuAr	DuAr	TYR- 147	3.95	0	Aromatic Face/Face	false
C3'	CD1	LEU- 150	4.38	0	Hydrophobic	false
N6	OD1	ASP- 196	3.31	144.58	H-Bond (Ligand Donor)	false
N1	N	LEU- 197	3.06	175.25	H-Bond (Protein Donor)	false
N	O	GLU- 224	3.17	152.49	H-Bond (Ligand Donor)	false
N	OE1	GLU- 224	3.46	175.28	H-Bond (Ligand Donor)	false
N	OE1	GLU- 224	3.46	0	Ionic (Ligand Cationic)	false
C1'	CB	SER- 226	4.31	0	Hydrophobic	false
C5'	CB	SER- 226	4.03	0	Hydrophobic	false
CE	CE1	TYR- 229	3.9	0	Hydrophobic	false
C5'	CE1	TYR- 229	3.99	0	Hydrophobic	false