scPDB - 3pdn entry

Protein Data Bank Entry:

PDB ID : 3pdn

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2010-10-23

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 SMYD3
ID:	SMYD3_HUMAN
AC:	Q9H7B4
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.1.1.43

Chains:

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

Ligand binding site composition:

B-Factor:	12.283
Number of residues:	34
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.750	1755.000

% Hydrophobic	% Polar
32.69	67.31
According to VolSite

Ligand :

HET Code:	SFG
Formula:	C15H24N7O5
Molecular weight:	382.395 g/mol
DrugBank ID:	DB01910
Buried Surface Area:	71.01 %
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
16.5751	19.3579	23.1212

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
N	O	ASN- 16	2.85	171.48	H-Bond (Ligand Donor)	false
O	N	ASN- 16	2.8	144.64	H-Bond (Protein Donor)	false
OXT	OH	TYR- 124	2.65	141.94	H-Bond (Protein Donor)	false
C4'	CG	GLU- 130	4.41	0	Hydrophobic	false
O3'	ND2	ASN- 132	2.92	134.28	H-Bond (Protein Donor)	false
O2'	ND2	ASN- 132	3.37	147.35	H-Bond (Protein Donor)	false
NE	OD1	ASN- 181	3.03	154.76	H-Bond (Ligand Donor)	false
NE	O	SER- 202	2.95	145	H-Bond (Ligand Donor)	false
N	OD1	ASN- 205	2.83	145.27	H-Bond (Ligand Donor)	false
N7	N	HIS- 206	2.94	172.16	H-Bond (Protein Donor)	false
N6	O	HIS- 206	2.91	149.42	H-Bond (Ligand Donor)	false
NE	OH	TYR- 239	3.47	122.92	H-Bond (Ligand Donor)	false
C5'	CE2	TYR- 239	4.03	0	Hydrophobic	false
C3'	CB	TYR- 257	4.01	0	Hydrophobic	false
O3'	O	TYR- 257	2.63	155.52	H-Bond (Ligand Donor)	false
DuAr	DuAr	PHE- 259	3.61	0	Aromatic Face/Face	false
C2'	CD2	PHE- 259	3.74	0	Hydrophobic	false
O2'	O	HOH- 725	2.72	152.01	H-Bond (Ligand Donor)	false