scPDB - 4dcm entry

Protein Data Bank Entry:

PDB ID : 4dcm

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2012-01-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Ribosomal RNA large subunit methyltransferase G
ID:	RLMG_ECOLI
AC:	P42596
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	2.1.1.174

Chains:

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

Ligand binding site composition:

B-Factor:	27.252
Number of residues:	41
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.542	428.625

% Hydrophobic	% Polar
48.82	51.18
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	59.57 %
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
39.0318	-2.1277	47.4777

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
SD	CD2	PHE- 208	3.49	0	Hydrophobic	false
CE	CZ	PHE- 208	3.65	0	Hydrophobic	false
C3'	CB	PHE- 208	4.43	0	Hydrophobic	false
CB	CD2	PHE- 208	3.59	0	Hydrophobic	false
N	OD1	ASP- 234	3.87	0	Ionic (Ligand Cationic)	false
N	O	GLY- 236	2.77	163.5	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 259	2.82	170.81	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 259	2.81	170.49	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 259	3.48	134.55	H-Bond (Ligand Donor)	false
N3	N	GLU- 260	3.25	135.01	H-Bond (Protein Donor)	false
N6	OD1	ASN- 289	3.23	166.85	H-Bond (Ligand Donor)	false
N1	N	ALA- 290	2.76	155.61	H-Bond (Protein Donor)	false
OXT	ND2	ASN- 305	3.01	159.25	H-Bond (Protein Donor)	false
CG	CB	ASN- 305	3.8	0	Hydrophobic	false
C5'	CG	PRO- 307	4.25	0	Hydrophobic	false
C1'	CE	MET- 322	4.42	0	Hydrophobic	false
N	O	HOH- 529	3.01	155.87	H-Bond (Ligand Donor)	false