scPDB - 4poo entry

Protein Data Bank Entry:

PDB ID : 4poo

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2014-02-26

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
ID:	E0TY72_BACPZ
AC:	E0TY72
Organism:	Bacillus subtilis subsp. spizizenii
Reign:	Bacteria
TaxID:	655816
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	55.346
Number of residues:	38
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.426	398.250

% Hydrophobic	% Polar
40.68	59.32
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	80.31 %
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
9.07541	26.5541	126.519

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
N	O	THR- 28	3.3	142.38	H-Bond (Ligand Donor)	false
CG	CB	THR- 28	4.19	0	Hydrophobic	false
C4'	CB	THR- 28	4.02	0	Hydrophobic	false
OXT	N	ASN- 31	2.94	153.06	H-Bond (Protein Donor)	false
O	ND1	HIS- 33	3.26	142.68	H-Bond (Protein Donor)	false
O	N	HIS- 33	2.96	149.39	H-Bond (Protein Donor)	false
N	OD2	ASP- 34	3.12	0	Ionic (Ligand Cationic)	false
O3'	OD2	ASP- 52	2.9	174.54	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 52	2.53	148.43	H-Bond (Ligand Donor)	false
O2'	NE2	GLN- 54	2.81	157.63	H-Bond (Protein Donor)	false
N6	OG	SER- 79	2.97	149.92	H-Bond (Ligand Donor)	false
N1	N	HIS- 80	2.96	158.32	H-Bond (Protein Donor)	false
DuAr	DuAr	HIS- 80	3.74	0	Aromatic Face/Face	false
CE	CB	ASN- 101	4.34	0	Hydrophobic	false
CB	CB	ASN- 101	3.83	0	Hydrophobic	false
C3'	CB	LEU- 105	3.94	0	Hydrophobic	false
C1'	CG2	THR- 114	4.18	0	Hydrophobic	false
N	O	HOH- 401	3.09	134.39	H-Bond (Ligand Donor)	false
N	O	HOH- 402	3.11	141.3	H-Bond (Ligand Donor)	false