scPDB - 1xva entry

Protein Data Bank Entry:

PDB ID : 1xva

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 1996-07-20

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	98 %
B	2 %

Ligand binding site composition:

B-Factor:	24.214
Number of residues:	43
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.513	668.250

% Hydrophobic	% Polar
34.34	65.66
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	53.66 %
Polar Surface area:	189.77 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	4
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
61.2865	74.5269	10.0698

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
N3	OH	TYR- 33	3.09	128.77	H-Bond (Protein Donor)	false
N	OD2	ASP- 70	2.89	0	Ionic (Ligand Cationic)	false
O3'	NE2	HIS- 142	3.49	139.23	H-Bond (Protein Donor)	false
N6	O	PRO- 187	2.78	133.37	H-Bond (Ligand Donor)	false
N1	N	GLY- 189	3.37	154.01	H-Bond (Protein Donor)	false
O2'	OH	TYR- 242	2.62	136.65	H-Bond (Protein Donor)	false
O	O	HOH- 343	2.91	144.32	H-Bond (Protein Donor)	false
N	O	HOH- 353	2.85	138.2	H-Bond (Ligand Donor)	false