scPDB - 5k7u entry

Protein Data Bank Entry:

PDB ID : 5k7u

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2016-05-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	N6-adenosine-methyltransferase 70 kDa subunit
ID:	MTA70_HUMAN
AC:	Q86U44
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	21.300
Number of residues:	32
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.448	702.000

% Hydrophobic	% Polar
34.62	65.38
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	66.09 %
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
-21.2521	30.0561	-1.86148

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
N6	OD1	ASP- 377	3.06	159.25	H-Bond (Ligand Donor)	false
N1	N	ILE- 378	2.95	172.72	H-Bond (Protein Donor)	false
N	OD2	ASP- 395	2.79	165.45	H-Bond (Ligand Donor)	false
N	OD2	ASP- 395	2.79	0	Ionic (Ligand Cationic)	false
CG	CB	ASP- 395	4.03	0	Hydrophobic	false
O	N	LYS- 513	2.93	163.8	H-Bond (Protein Donor)	false
N	OE1	GLU- 532	3.99	0	Ionic (Ligand Cationic)	false
C1'	CD1	PHE- 534	4.28	0	Hydrophobic	false
C4'	CB	PHE- 534	3.89	0	Hydrophobic	false
OXT	CZ	ARG- 536	3.98	0	Ionic (Protein Cationic)	false
OXT	NH1	ARG- 536	3.16	125.41	H-Bond (Protein Donor)	false
C3'	CD	ARG- 536	4.43	0	Hydrophobic	false
CB	CD	ARG- 536	3.79	0	Hydrophobic	false
O	NE2	HIS- 538	3.2	154.03	H-Bond (Protein Donor)	false
O	ND2	ASN- 539	3.13	159.95	H-Bond (Protein Donor)	false
O2'	OD1	ASN- 549	2.6	166.42	H-Bond (Ligand Donor)	false
N3	N	ASN- 549	3.17	128.85	H-Bond (Protein Donor)	false
O3'	OE1	GLN- 550	2.6	159.7	H-Bond (Ligand Donor)	false
N	O	HOH- 725	2.88	156.57	H-Bond (Ligand Donor)	false
O3'	O	HOH- 748	2.95	169.21	H-Bond (Protein Donor)	false