scPDB - 3c3y entry

Protein Data Bank Entry:

PDB ID : 3c3y

Resolution :1.370 Å

Experimental Method : X-ray

Deposition Date : 2008-01-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	O-methyltransferase
ID:	Q6YI95_MESCR
AC:	Q6YI95
Organism:	Mesembryanthemum crystallinum
Reign:	Eukaryota
TaxID:	3544
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	13.691
Number of residues:	38
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:	CA

Cavity properties

Ligandability	Volume (Å3)
0.553	651.375

% Hydrophobic	% Polar
48.70	51.30
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	74.05 %
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
-3.65219	4.62369	30.6699

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
C3'	CE	MET- 52	4.27	0	Hydrophobic	false
SD	SD	MET- 52	3.92	0	Hydrophobic	false
OXT	OG1	THR- 54	2.62	164.69	H-Bond (Protein Donor)	false
OXT	N	THR- 54	3.14	144.39	H-Bond (Protein Donor)	false
N	O	GLY- 78	2.92	161.81	H-Bond (Ligand Donor)	false
SD	CB	PHE- 80	3.81	0	Hydrophobic	false
C3'	CB	PHE- 80	4.37	0	Hydrophobic	false
CB	CB	PHE- 80	3.51	0	Hydrophobic	false
N	OG	SER- 84	2.89	156.05	H-Bond (Ligand Donor)	false
OXT	N	SER- 84	3.19	161.89	H-Bond (Protein Donor)	false
O3'	OD1	ASP- 102	3.32	137.16	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 102	2.69	164.08	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 102	2.74	160.86	H-Bond (Ligand Donor)	false
N3	N	PHE- 103	3.23	148.91	H-Bond (Protein Donor)	false
DuAr	DuAr	PHE- 103	3.68	0	Aromatic Face/Face	false
C2'	CE1	PHE- 103	3.86	0	Hydrophobic	false
N6	OD1	ASP- 130	3.3	159.33	H-Bond (Ligand Donor)	false
N1	N	ALA- 131	2.84	147.57	H-Bond (Protein Donor)	false
N	OD2	ASP- 154	2.82	160.97	H-Bond (Ligand Donor)	false
N	OD2	ASP- 154	2.82	0	Ionic (Ligand Cationic)	false
CG	CB	ASP- 154	4.48	0	Hydrophobic	false
C1'	CB	ALA- 155	4.44	0	Hydrophobic	false
O	O	HOH- 466	2.52	159.4	H-Bond (Protein Donor)	false
N6	O	HOH- 483	3.41	127.09	H-Bond (Ligand Donor)	false