scPDB - 3m53 entry

Protein Data Bank Entry:

PDB ID : 3m53

Resolution :1.850 Å

Experimental Method : X-ray

Deposition Date : 2010-03-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Histone-lysine N-methyltransferase SETD7
ID:	SETD7_HUMAN
AC:	Q8WTS6
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.1.1.43

Chains:

Chain Name:	Percentage of Residues within binding site
A	96 %
B	4 %

Ligand binding site composition:

B-Factor:	37.133
Number of residues:	28
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.486	661.500

% Hydrophobic	% Polar
32.65	67.35
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	59.97 %
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
-28.8088	18.6647	-6.89854

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	GLU- 228	2.81	137.36	H-Bond (Ligand Donor)	false
OXT	N	GLU- 228	2.89	141	H-Bond (Protein Donor)	false
CB	CD	LYS- 294	4.27	0	Hydrophobic	false
O	NZ	LYS- 294	2.82	147.02	H-Bond (Protein Donor)	false
O	NZ	LYS- 294	2.82	0	Ionic (Protein Cationic)	false
OXT	NZ	LYS- 294	3.69	0	Ionic (Protein Cationic)	false
N	OD1	ASN- 296	2.91	169.62	H-Bond (Ligand Donor)	false
N7	N	HIS- 297	2.93	168.21	H-Bond (Protein Donor)	false
N6	O	HIS- 297	2.96	143.89	H-Bond (Ligand Donor)	false
C5'	CE2	TYR- 335	4.08	0	Hydrophobic	false
C3'	CZ2	TRP- 352	3.81	0	Hydrophobic	false
C2'	CE2	TRP- 352	3.68	0	Hydrophobic	false
DuAr	DuAr	TRP- 352	3.87	0	Aromatic Face/Face	false
N6	OE2	GLU- 356	3.31	148.69	H-Bond (Ligand Donor)	false