scPDB - 3dlc entry

Protein Data Bank Entry:

PDB ID : 3dlc

Resolution :1.150 Å

Experimental Method : X-ray

Deposition Date : 2008-06-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	SAM (And some other nucleotide) binding motif:Generic methyltransferase
ID:	Q6LY14_METMP
AC:	Q6LY14
Organism:	Methanococcus maripaludis
Reign:	Archaea
TaxID:	267377
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	8.858
Number of residues:	36
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.886	918.000

% Hydrophobic	% Polar
50.00	50.00
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	73.91 %
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
2.28641	2.32159	18.2795

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
C5'	CE1	PHE- 8	4.3	0	Hydrophobic	false
C2'	CD1	PHE- 8	3.73	0	Hydrophobic	false
CB	CG	MET- 16	4.4	0	Hydrophobic	false
CE	SD	MET- 16	3.65	0	Hydrophobic	false
SD	SD	MET- 16	3.8	0	Hydrophobic	false
OXT	OH	TYR- 28	2.69	132.73	H-Bond (Protein Donor)	false
N	O	GLY- 50	2.83	163.08	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 72	2.63	158.89	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 72	2.71	154.28	H-Bond (Ligand Donor)	false
N3	N	PHE- 73	3.35	152.67	H-Bond (Protein Donor)	false
DuAr	DuAr	PHE- 73	3.74	0	Aromatic Face/Face	false
C2'	CE1	PHE- 73	3.83	0	Hydrophobic	false
C3'	CE	MET- 77	3.84	0	Hydrophobic	false
N6	OD1	ASP- 100	3.05	159.01	H-Bond (Ligand Donor)	false
N1	N	VAL- 101	3.19	168.3	H-Bond (Protein Donor)	false
N	O	ARG- 117	2.95	163.15	H-Bond (Ligand Donor)	false
O	NH1	ARG- 117	2.96	163.7	H-Bond (Protein Donor)	false
O	CZ	ARG- 117	3.92	0	Ionic (Protein Cationic)	false
O4'	OG	SER- 119	2.8	167.34	H-Bond (Protein Donor)	false
C4'	CB	SER- 119	4.27	0	Hydrophobic	false
CE	CE2	PHE- 122	4.19	0	Hydrophobic	false
C5'	CE2	PHE- 122	4.31	0	Hydrophobic	false
OXT	O	HOH- 297	2.88	176.72	H-Bond (Protein Donor)	false