scPDB - 1y6r entry

Protein Data Bank Entry:

PDB ID : 1y6r

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2004-12-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
ID:	MTNN_ECOLI
AC:	P0AF12
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	3.2.2.9

Chains:

Chain Name:	Percentage of Residues within binding site
A	12 %
B	88 %

Ligand binding site composition:

B-Factor:	21.469
Number of residues:	36
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.685	280.125

% Hydrophobic	% Polar
66.27	33.73
According to VolSite

Ligand :

HET Code:	MTM
Formula:	C12H22N5O2S
Molecular weight:	300.400 g/mol
DrugBank ID:	DB02158
Buried Surface Area:	83.7 %
Polar Surface area:	151.8 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	7
Rings:	3
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	3
Rule of Five Violation:	1
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
45.6377	86.3535	41.9489

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
C3'	CG2	ILE- 50	4.1	0	Hydrophobic	false
CS	CD1	ILE- 50	3.91	0	Hydrophobic	false
N4'	OG	SER- 76	3.26	120.13	H-Bond (Ligand Donor)	false
S5'	CG1	VAL- 102	4.35	0	Hydrophobic	false
CS	CE2	PHE- 105	3.72	0	Hydrophobic	false
C5'	CD2	PHE- 151	3.7	0	Hydrophobic	false
N6	O	ILE- 152	3.15	141.1	H-Bond (Ligand Donor)	false
N1	N	ILE- 152	2.88	171.96	H-Bond (Protein Donor)	false
C2'	CB	GLU- 172	3.88	0	Hydrophobic	false
C2'	CB	MET- 173	3.72	0	Hydrophobic	false
C3'	SD	MET- 173	3.78	0	Hydrophobic	false
S5'	SD	MET- 173	3.69	0	Hydrophobic	false
O2'	N	MET- 173	2.66	141.7	H-Bond (Protein Donor)	false
O2'	OE1	GLU- 174	3.3	150.88	H-Bond (Ligand Donor)	false
O2'	OE2	GLU- 174	2.72	136.72	H-Bond (Ligand Donor)	false
O3'	OE1	GLU- 174	2.65	150.02	H-Bond (Ligand Donor)	false
O2'	NH1	ARG- 193	3.38	121.59	H-Bond (Protein Donor)	false
N7	OD2	ASP- 197	2.68	152.44	H-Bond (Ligand Donor)	false
N6	OD1	ASP- 197	2.95	165.61	H-Bond (Ligand Donor)	false
CS	CE1	PHE- 207	3.88	0	Hydrophobic	false
C5'	CZ	PHE- 207	4.07	0	Hydrophobic	false