scPDB - 3n71 entry

Protein Data Bank Entry:

PDB ID : 3n71

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2010-05-26

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 Smyd1
ID:	SMYD1_MOUSE
AC:	P97443
Organism:	Mus musculus
Reign:	Eukaryota
TaxID:	10090
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	57.818
Number of residues:	29
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.862	742.500

% Hydrophobic	% Polar
41.36	58.64
According to VolSite

Ligand :

HET Code:	SFG
Formula:	C15H24N7O5
Molecular weight:	382.395 g/mol
DrugBank ID:	DB01910
Buried Surface Area:	65.51 %
Polar Surface area:	214.71 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	5
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
47.85	65.4523	30.9712

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	ARG- 19	2.68	171.19	H-Bond (Ligand Donor)	false
O	CZ	ARG- 19	3.68	0	Ionic (Protein Cationic)	false
OXT	CZ	ARG- 19	3.94	0	Ionic (Protein Cationic)	false
OXT	NE	ARG- 19	3.17	141.08	H-Bond (Protein Donor)	false
OXT	N	ARG- 19	2.97	143.11	H-Bond (Protein Donor)	false
OXT	NE2	GLN- 133	3.29	123.38	H-Bond (Protein Donor)	false
O2'	OE1	GLN- 133	2.57	161.34	H-Bond (Ligand Donor)	false
O3'	NE2	HIS- 135	2.94	127.65	H-Bond (Protein Donor)	false
O2'	NE2	HIS- 135	2.67	145.32	H-Bond (Protein Donor)	false
NE	O	GLY- 202	2.8	156.33	H-Bond (Ligand Donor)	false
N	OD1	ASN- 205	2.93	137.83	H-Bond (Ligand Donor)	false
N7	N	HIS- 206	2.98	170.67	H-Bond (Protein Donor)	false
N6	O	HIS- 206	3.06	153.63	H-Bond (Ligand Donor)	false
C3'	CB	TYR- 270	4.25	0	Hydrophobic	false
O3'	O	TYR- 270	3.34	150.19	H-Bond (Ligand Donor)	false
DuAr	DuAr	PHE- 272	3.72	0	Aromatic Face/Face	false
C2'	CD1	PHE- 272	3.83	0	Hydrophobic	false