scPDB - 5bxy entry

Protein Data Bank Entry:

PDB ID : 5bxy

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 2015-06-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative RNA methylase family UPF0020
ID:	Q2S3S9_SALRD
AC:	Q2S3S9
Organism:	Salinibacter ruber
Reign:	Bacteria
TaxID:	309807
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	97 %
B	3 %

Ligand binding site composition:

B-Factor:	14.130
Number of residues:	37
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.518	418.500

% Hydrophobic	% Polar
49.19	50.81
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	75.17 %
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
19.4548	18.7526	60.0153

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
C5'	CG1	VAL- 2	3.65	0	Hydrophobic	false
SD	CD1	TYR- 4	4.08	0	Hydrophobic	false
C3'	CB	TYR- 4	4.1	0	Hydrophobic	false
O	N	THR- 7	2.89	166.12	H-Bond (Protein Donor)	false
OXT	OG1	THR- 7	2.66	167.31	H-Bond (Protein Donor)	false
N	OD1	ASP- 29	3.38	122.33	H-Bond (Ligand Donor)	false
N	OD2	ASP- 29	2.89	156.99	H-Bond (Ligand Donor)	false
N	OD1	ASP- 29	3.38	0	Ionic (Ligand Cationic)	false
N	OD2	ASP- 29	2.89	0	Ionic (Ligand Cationic)	false
N	O	GLY- 31	2.76	161.16	H-Bond (Ligand Donor)	false
O3'	OE1	GLU- 53	2.66	170.89	H-Bond (Ligand Donor)	false
O3'	OE2	GLU- 53	3.45	122.28	H-Bond (Ligand Donor)	false
O2'	OE2	GLU- 53	2.57	154.01	H-Bond (Ligand Donor)	false
C1'	CG2	ILE- 54	4.46	0	Hydrophobic	false
N3	N	ILE- 54	3.25	138.79	H-Bond (Protein Donor)	false
C3'	CD1	LEU- 58	4.43	0	Hydrophobic	false
N6	OD1	ASP- 81	2.93	176.21	H-Bond (Ligand Donor)	false
N1	N	LEU- 82	2.86	171.44	H-Bond (Protein Donor)	false
CG	CD2	TYR- 96	4.07	0	Hydrophobic	false