scPDB - 4dkj entry

Protein Data Bank Entry:

PDB ID : 4dkj

Resolution :2.150 Å

Experimental Method : X-ray

Deposition Date : 2012-02-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cytosine-specific methyltransferase
ID:	Q8EVR5_MYCPE
AC:	Q8EVR5
Organism:	Mycoplasma penetrans
Reign:	Bacteria
TaxID:	272633
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	21.825
Number of residues:	39
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.004	523.125

% Hydrophobic	% Polar
36.13	63.87
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	79.83 %
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
28.4761	26.2187	42.9026

Binding mode :

What is Poseview ?

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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
C1'	CD1	PHE- 17	4.2	0	Hydrophobic	false
C4'	CB	PHE- 17	3.97	0	Hydrophobic	false
OXT	N	ILE- 20	3.06	156.66	H-Bond (Protein Donor)	false
O	N	SER- 22	3	164.92	H-Bond (Protein Donor)	false
O	OG	SER- 22	2.76	159.6	H-Bond (Protein Donor)	false
N	OE1	GLN- 23	2.77	143.76	H-Bond (Ligand Donor)	false
O3'	OE1	GLU- 45	3.01	169.57	H-Bond (Ligand Donor)	false
O3'	OE2	GLU- 45	3.39	135.78	H-Bond (Ligand Donor)	false
O2'	OE2	GLU- 45	2.76	160.82	H-Bond (Ligand Donor)	false
C2'	CB	SER- 80	4.45	0	Hydrophobic	false
N6	OD1	ASP- 113	3.17	165.38	H-Bond (Ligand Donor)	false
N1	N	ILE- 114	3.1	161.61	H-Bond (Protein Donor)	false
N	OG	SER- 132	2.7	157.37	H-Bond (Ligand Donor)	false
CG	CB	SER- 132	4.23	0	Hydrophobic	false
N7	NH2	ARG- 154	3.28	154.56	H-Bond (Protein Donor)	false
CB	CB	ASN- 374	4.42	0	Hydrophobic	false
SD	CB	ASN- 374	3.92	0	Hydrophobic	false
O	OG	SER- 375	3.06	154.83	H-Bond (Protein Donor)	false
OXT	OG	SER- 375	3.11	150.19	H-Bond (Protein Donor)	false
OXT	O	HOH- 612	2.54	161.57	H-Bond (Protein Donor)	false