scPDB - 3dz6 entry

Protein Data Bank Entry:

PDB ID : 3dz6

Resolution :1.830 Å

Experimental Method : X-ray

Deposition Date : 2008-07-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	S-adenosylmethionine decarboxylase proenzyme
ID:	DCAM_HUMAN
AC:	P17707
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	4.1.1.50

Chains:

Chain Name:	Percentage of Residues within binding site
B	39 %
A	61 %

Ligand binding site composition:

B-Factor:	27.069
Number of residues:	35
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.543	415.125

% Hydrophobic	% Polar
46.34	53.66
According to VolSite

Ligand :

HET Code:	M8E
Formula:	C17H28N7O4
Molecular weight:	394.449 g/mol
DrugBank ID:	DB08163
Buried Surface Area:	70.26 %
Polar Surface area:	158.99 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
-17.176	-5.81996	6.05257

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
C6	CZ	PHE- 7	3.89	0	Hydrophobic	false
C4'	CE2	PHE- 7	4.49	0	Hydrophobic	false
C2'	CG	PHE- 7	3.87	0	Hydrophobic	false
C3'	CD2	PHE- 7	3.91	0	Hydrophobic	false
N7	OG	SER- 66	2.96	123.59	H-Bond (Ligand Donor)	false
N4	N	GLU- 67	3.09	156.85	H-Bond (Protein Donor)	false
N7	O	GLU- 67	3.27	140.64	H-Bond (Ligand Donor)	false
C5	SG	CYS- 82	4.17	0	Hydrophobic	false
C1'	CB	PHE- 223	4.25	0	Hydrophobic	false
C5	CZ	PHE- 223	4.04	0	Hydrophobic	false
C4'	CB	THR- 245	4.41	0	Hydrophobic	false
C3'	CG2	THR- 245	3.81	0	Hydrophobic	false
O2'	OE2	GLU- 247	3.02	153.63	H-Bond (Ligand Donor)	false
O3'	OE1	GLU- 247	2.67	147.88	H-Bond (Ligand Donor)	false