scPDB - 2idk entry

Protein Data Bank Entry:

PDB ID : 2idk

Resolution :2.550 Å

Experimental Method : X-ray

Deposition Date : 2006-09-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glycine N-methyltransferase
ID:	GNMT_RAT
AC:	P13255
Organism:	Rattus norvegicus
Reign:	Eukaryota
TaxID:	10116
EC Number:	2.1.1.20

Chains:

Chain Name:	Percentage of Residues within binding site
A	26 %
B	23 %
C	35 %
D	16 %

Ligand binding site composition:

B-Factor:	56.636
Number of residues:	31
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.148	560.250

% Hydrophobic	% Polar
57.23	42.77
According to VolSite

Ligand :

HET Code:	C2F
Formula:	C20H23N7O6
Molecular weight:	457.440 g/mol
DrugBank ID:	-
Buried Surface Area:	47.26 %
Polar Surface area:	204.14 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	5
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
12.3357	-8.23733	45.3579

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
C9	CG	TYR- 5	3.65	0	Hydrophobic	false
C11	CB	TYR- 5	4.17	0	Hydrophobic	false
CB	CZ	TYR- 5	3.29	0	Hydrophobic	false
CG	CE2	TYR- 5	3.91	0	Hydrophobic	false
C7	CD1	TYR- 5	3.55	0	Hydrophobic	false
C16	CG	TYR- 5	3.32	0	Hydrophobic	false
C12	CB	TYR- 5	3.65	0	Hydrophobic	false
C16	CD1	LEU- 207	4.21	0	Hydrophobic	false
CB	CD2	LEU- 207	4.39	0	Hydrophobic	false
C17	CD1	LEU- 207	4.11	0	Hydrophobic	false
C9	CD2	LEU- 207	3.62	0	Hydrophobic	false
N8	NE2	HIS- 214	3.43	137.64	H-Bond (Ligand Donor)	false
C9	SD	MET- 215	4.42	0	Hydrophobic	false
C15	CE	MET- 215	3.36	0	Hydrophobic	false
O	NH2	ARG- 239	3.38	160.58	H-Bond (Protein Donor)	false