scPDB - 1d2h entry

Protein Data Bank Entry:

PDB ID : 1d2h

Resolution :3.000 Å

Experimental Method : X-ray

Deposition Date : 1999-10-11

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
C	100 %

Ligand binding site composition:

B-Factor:	18.906
Number of residues:	31
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.760	671.625

% Hydrophobic	% Polar
38.19	61.81
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	54.5 %
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
13.8515	13.7477	-14.2848

Binding mode :

What is Poseview ?

2D View
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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
O3'	OD1	ASP- 85	2.93	165.57	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 85	2.69	124.93	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 85	2.79	177.47	H-Bond (Ligand Donor)	false
N3	N	ALA- 86	3.22	141.5	H-Bond (Protein Donor)	false
C2'	CB	SER- 87	3.95	0	Hydrophobic	false
C3'	SD	MET- 90	4.36	0	Hydrophobic	false
N6	OD1	ASN- 116	3.04	154.95	H-Bond (Ligand Donor)	false
N1	N	TRP- 117	3.32	158.47	H-Bond (Protein Donor)	false
DuAr	DuAr	TRP- 117	3.78	0	Aromatic Face/Face	false
SD	CB	SER- 139	4.1	0	Hydrophobic	false