scPDB - 2zfu entry

Protein Data Bank Entry:

PDB ID : 2zfu

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2008-01-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Ribosomal RNA-processing protein 8
ID:	RRP8_HUMAN
AC:	O43159
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	32.624
Number of residues:	50
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	7
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.022	317.250

% Hydrophobic	% Polar
55.32	44.68
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	75.57 %
Polar Surface area:	212.38 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
17.5208	8.21604	-4.23088

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
C3'	CE2	TYR- 280	3.98	0	Hydrophobic	false
SD	CE2	TYR- 280	3.85	0	Hydrophobic	false
O3'	NE2	HIS- 281	2.82	126.21	H-Bond (Protein Donor)	false
CB	CE2	PHE- 284	4.35	0	Hydrophobic	false
CG	CZ	PHE- 284	3.69	0	Hydrophobic	false
SD	CE1	PHE- 284	3.79	0	Hydrophobic	false
N	O	GLY- 316	2.94	161.97	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 334	3.31	122.58	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 334	2.66	158.34	H-Bond (Ligand Donor)	false
N6	OD1	ASP- 346	3.02	173.45	H-Bond (Ligand Donor)	false
N1	N	MET- 347	2.91	162.4	H-Bond (Protein Donor)	false
N	O	CYS- 363	2.88	163.94	H-Bond (Ligand Donor)	false
CG	CB	LEU- 364	4.18	0	Hydrophobic	false
C4'	CB	SER- 365	4.31	0	Hydrophobic	false
C5'	SD	MET- 367	4.03	0	Hydrophobic	false
C2'	SD	MET- 367	4.2	0	Hydrophobic	false
O	O	HOH- 906	2.84	179.95	H-Bond (Protein Donor)	false
OXT	O	HOH- 915	2.83	179.96	H-Bond (Protein Donor)	false
N	O	HOH- 920	2.85	158.91	H-Bond (Ligand Donor)	false
OXT	O	HOH- 952	2.58	179.97	H-Bond (Protein Donor)	false