scPDB - 4dmg entry

Protein Data Bank Entry:

PDB ID : 4dmg

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2012-02-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Uncharacterized protein
ID:	Q5SI81_THET8
AC:	Q5SI81
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	300852
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	18.169
Number of residues:	35
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.782	1572.750

% Hydrophobic	% Polar
37.12	62.88
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	65.61 %
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
59.8002	22.3047	74.4125

Binding mode :

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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
O2'	NE2	GLN- 193	2.95	154.22	H-Bond (Protein Donor)	false
SD	CE2	TYR- 198	3.55	0	Hydrophobic	false
CE	CE1	TYR- 198	3.85	0	Hydrophobic	false
CB	CD2	TYR- 198	3.64	0	Hydrophobic	false
OXT	NH1	ARG- 205	2.95	141.04	H-Bond (Protein Donor)	false
N	O	TYR- 222	3.03	150.73	H-Bond (Ligand Donor)	false
CG	CB	TYR- 222	4.37	0	Hydrophobic	false
C1'	CD1	TYR- 222	4.15	0	Hydrophobic	false
C4'	CB	TYR- 222	3.8	0	Hydrophobic	false
C3'	CB	TYR- 224	4.49	0	Hydrophobic	false
CB	CB	TYR- 224	3.69	0	Hydrophobic	false
O3'	OD2	ASP- 243	2.82	168.28	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 243	2.7	158.85	H-Bond (Ligand Donor)	false
N3	N	LYS- 244	3.39	145.22	H-Bond (Protein Donor)	false
N1	N	ALA- 270	2.86	148.84	H-Bond (Protein Donor)	false
N	OD2	ASP- 287	2.75	176.44	H-Bond (Ligand Donor)	false
N	OD2	ASP- 287	2.75	0	Ionic (Ligand Cationic)	false
CG	CB	ASP- 287	4.14	0	Hydrophobic	false
C5'	CB	PRO- 289	4.49	0	Hydrophobic	false