scPDB - 2plm entry

Protein Data Bank Entry:

PDB ID : 2plm

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2007-04-20

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 deaminase
ID:	MTAD_THEMA
AC:	Q9X034
Organism:	Thermotoga maritima
Reign:	Bacteria
TaxID:	243274
EC Number:	3.5.4.28

Chains:

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

Ligand binding site composition:

B-Factor:	29.051
Number of residues:	35
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.455	526.500

% Hydrophobic	% Polar
55.77	44.23
According to VolSite

Ligand :

HET Code:	SIB
Formula:	C14H19N5O6S
Molecular weight:	385.396 g/mol
DrugBank ID:	-
Buried Surface Area:	75.54 %
Polar Surface area:	202.03 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
45.4167	31.9868	-1.48492

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
C2'	SD	MET- 60	3.96	0	Hydrophobic	false
C1'	CD1	LEU- 76	4.47	0	Hydrophobic	false
O3'	OE1	GLU- 84	2.71	168.54	H-Bond (Ligand Donor)	false
O2'	OE1	GLU- 84	3.28	120.53	H-Bond (Ligand Donor)	false
O2'	OE2	GLU- 84	2.72	174.71	H-Bond (Ligand Donor)	false
C5'	SD	MET- 114	3.91	0	Hydrophobic	false
C5'	CD1	TYR- 115	4.28	0	Hydrophobic	false
C3'	CE1	TYR- 115	3.88	0	Hydrophobic	false
O	CZ	ARG- 136	3.69	0	Ionic (Protein Cationic)	false
O	NH1	ARG- 136	3.04	144.83	H-Bond (Protein Donor)	false
CB	CG1	VAL- 139	4.32	0	Hydrophobic	false
OXT	CZ	ARG- 148	3.8	0	Ionic (Protein Cationic)	false
O	CZ	ARG- 148	3.51	0	Ionic (Protein Cationic)	false
OXT	NH2	ARG- 148	3.03	156.07	H-Bond (Protein Donor)	false
O	NE	ARG- 148	2.75	171.18	H-Bond (Protein Donor)	false
O	NH2	ARG- 148	3.41	129.92	H-Bond (Protein Donor)	false
N3	NE2	HIS- 173	3.03	149.25	H-Bond (Ligand Donor)	false
O6	O	HOH- 409	2.94	121.69	H-Bond (Protein Donor)	false
N7	O	HOH- 442	2.72	179.96	H-Bond (Protein Donor)	false