scPDB - 4rtm entry

Protein Data Bank Entry:

PDB ID : 4rtm

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2014-11-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	DNA adenine methylase
ID:	DMA_ECOLI
AC:	P0AEE8
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	2.1.1.72

Chains:

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

Ligand binding site composition:

B-Factor:	40.978
Number of residues:	33
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.731	648.000

% Hydrophobic	% Polar
47.40	52.60
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	68.6 %
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
-1.50041	-1.19633	89.0219

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
O3'	NE1	TRP- 10	2.81	161.09	H-Bond (Protein Donor)	false
N	O	PHE- 35	3.49	128.32	H-Bond (Ligand Donor)	false
C1'	CD2	PHE- 35	3.96	0	Hydrophobic	false
C4'	CB	PHE- 35	3.87	0	Hydrophobic	false
OXT	N	ALA- 38	2.81	154.2	H-Bond (Protein Donor)	false
O	OG	SER- 40	3.04	153.66	H-Bond (Protein Donor)	false
O3'	OD2	ASP- 54	3.23	163.66	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 54	3.35	141.28	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 54	2.64	157.45	H-Bond (Ligand Donor)	false
C1'	CG2	ILE- 55	4.49	0	Hydrophobic	false
N1	N	TYR- 165	3.17	131.92	H-Bond (Protein Donor)	false
CG	CB	ASP- 181	4.33	0	Hydrophobic	false
C5'	CG	PRO- 183	4.4	0	Hydrophobic	false