scPDB - 3s7d entry

Protein Data Bank Entry:

PDB ID : 3s7d

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2011-05-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	N-lysine methyltransferase SMYD2
ID:	SMYD2_HUMAN
AC:	Q9NRG4
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:	41.731
Number of residues:	50
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.809	735.750

% Hydrophobic	% Polar
38.99	61.01
According to VolSite

Ligand :

HET Code:	LEU_SER_LYS_LYS_MLZ
Formula:	C28H60N8O6
Molecular weight:	604.826 g/mol
DrugBank ID:	-
Buried Surface Area:	54.78 %
Polar Surface area:	253.22 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	9
Rings:	0
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	4
Rule of Five Violation:	3
Rotatable Bonds:	25

Mass center Coordinates

X	Y	Z
-18.9601	-50.2191	-25.4644

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
CD1	CD2	LEU- 108	4.36	0	Hydrophobic	false
N	O	GLY- 183	3.06	145.52	H-Bond (Ligand Donor)	false
CB	CD1	PHE- 184	4.16	0	Hydrophobic	false
CD	CZ	PHE- 184	4.28	0	Hydrophobic	false
CB	CG2	THR- 185	3.58	0	Hydrophobic	false
CB	CG2	THR- 185	3.42	0	Hydrophobic	false
O	N	THR- 185	3.47	166.45	H-Bond (Protein Donor)	false
N	OE1	GLU- 187	3.39	161.43	H-Bond (Ligand Donor)	false
N	OE2	GLU- 187	3.47	155.47	H-Bond (Ligand Donor)	false
CB	CD1	LEU- 191	3.73	0	Hydrophobic	false
CB	CB	LEU- 191	4.22	0	Hydrophobic	false
CD	CB	LEU- 191	4.39	0	Hydrophobic	false
CD1	CB	SER- 196	3.69	0	Hydrophobic	false
CG	CG	TYR- 240	3.86	0	Hydrophobic	false
CD	CD1	TYR- 240	3.75	0	Hydrophobic	false
N	O	TYR- 240	3.35	147.72	H-Bond (Ligand Donor)	false
CG	CZ	TYR- 258	3.56	0	Hydrophobic	false
CD	CZ	TYR- 344	4.42	0	Hydrophobic	false
NZ	OH	TYR- 344	3.45	124.76	H-Bond (Ligand Donor)	false
CD	CD1	LEU- 379	3.51	0	Hydrophobic	false
CG	CB	LEU- 379	3.69	0	Hydrophobic	false
O	ND2	ASN- 380	3.46	165.28	H-Bond (Protein Donor)	false