scPDB - 3rib entry

Protein Data Bank Entry:

PDB ID : 3rib

Resolution :2.790 Å

Experimental Method : X-ray

Deposition Date : 2011-04-13

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
B	100 %

Ligand binding site composition:

B-Factor:	50.445
Number of residues:	30
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
1.301	1123.875

% Hydrophobic	% Polar
41.74	58.26
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	69.64 %
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
-3.08592	-51.7228	37.949

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	3	159.82	H-Bond (Ligand Donor)	false
O	NE	ARG- 19	2.71	165.68	H-Bond (Protein Donor)	false
O	NH2	ARG- 19	3.5	126.94	H-Bond (Protein Donor)	false
O	N	ARG- 19	3.12	129.45	H-Bond (Protein Donor)	false
OXT	NH2	ARG- 19	2.91	158.35	H-Bond (Protein Donor)	false
O	CZ	ARG- 19	3.53	0	Ionic (Protein Cationic)	false
OXT	CZ	ARG- 19	3.7	0	Ionic (Protein Cationic)	false
O2'	OE2	GLU- 135	3.26	148.68	H-Bond (Ligand Donor)	false
O3'	NE2	HIS- 137	2.73	132.41	H-Bond (Protein Donor)	false
O2'	NE2	HIS- 137	2.85	143.67	H-Bond (Protein Donor)	false
C3'	SG	CYS- 181	4.46	0	Hydrophobic	false
N7	N	HIS- 207	3.1	169.28	H-Bond (Protein Donor)	false
N6	O	HIS- 207	3.05	142.69	H-Bond (Ligand Donor)	false
C5'	CE2	TYR- 240	3.77	0	Hydrophobic	false
C3'	CB	TYR- 258	4.21	0	Hydrophobic	false
O3'	O	TYR- 258	2.99	164.05	H-Bond (Ligand Donor)	false
DuAr	DuAr	PHE- 260	3.82	0	Aromatic Face/Face	false
C2'	CD2	PHE- 260	3.73	0	Hydrophobic	false