scPDB - 1i7m entry

Protein Data Bank Entry:

PDB ID : 1i7m

Resolution :2.240 Å

Experimental Method : X-ray

Deposition Date : 2001-03-09

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	38 %
A	62 %

Ligand binding site composition:

B-Factor:	12.409
Number of residues:	28
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.501	334.125

% Hydrophobic	% Polar
40.40	59.60
According to VolSite

Ligand :

HET Code:	CG
Formula:	C11H16N6
Molecular weight:	232.285 g/mol
DrugBank ID:	-
Buried Surface Area:	72.14 %
Polar Surface area:	127.61 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	5
Rings:	2
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	2
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
23.0771	-3.52388	-39.0872

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
C10	CZ	PHE- 7	4.12	0	Hydrophobic	false
N6	O	LEU- 65	2.96	125.86	H-Bond (Ligand Donor)	false
N7	O	LEU- 65	2.78	130.47	H-Bond (Ligand Donor)	false
C8	SG	CYS- 82	4.17	0	Hydrophobic	false
C10	CD2	PHE- 223	3.78	0	Hydrophobic	false
C4	CE2	PHE- 223	3.33	0	Hydrophobic	false
N7	OG	SER- 229	2.87	136.01	H-Bond (Ligand Donor)	false
C8	CB	SER- 229	4.22	0	Hydrophobic	false
C9	CB	HIS- 243	3.88	0	Hydrophobic	false
N16	OE2	GLU- 247	3.13	130.05	H-Bond (Ligand Donor)	false