scPDB - 3q87 entry

Protein Data Bank Entry:

PDB ID : 3q87

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2011-01-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	N6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY)
ID:	Q8SRR4_ENCCU
AC:	Q8SRR4
Organism:	Encephalitozoon cuniculi
Reign:	Eukaryota
TaxID:	284813
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	20.738
Number of residues:	43
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.813	550.125

% Hydrophobic	% Polar
51.53	48.47
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	76.02 %
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
36.4584	13.2884	13.3285

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
SD	CG	TYR- 4	3.39	0	Hydrophobic	false
CE	CE1	TYR- 4	3.69	0	Hydrophobic	false
C3'	CB	TYR- 4	4.34	0	Hydrophobic	false
CG	CD2	TYR- 4	3.66	0	Hydrophobic	false
N	O	GLY- 31	2.7	162.99	H-Bond (Ligand Donor)	false
CB	CB	SER- 33	3.58	0	Hydrophobic	false
O3'	OD1	ASP- 51	2.71	151.42	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 51	2.58	166.94	H-Bond (Ligand Donor)	false
N3	N	LEU- 52	3.45	140.83	H-Bond (Protein Donor)	false
N6	OD1	ASP- 69	2.94	153.62	H-Bond (Ligand Donor)	false
N1	N	LEU- 70	2.89	172.11	H-Bond (Protein Donor)	false
OXT	ND2	ASN- 85	3.04	163.3	H-Bond (Protein Donor)	false
CG	CB	ASN- 85	3.93	0	Hydrophobic	false
C3'	CG2	ILE- 96	4.06	0	Hydrophobic	false
N	O	HOH- 171	3.44	176.11	H-Bond (Ligand Donor)	false