scPDB - 4x2d entry

Protein Data Bank Entry:

PDB ID : 4x2d

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2014-11-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Fic family protein putative filamentation induced by cAMP protein
ID:	C9YJ22_PEPDR
AC:	C9YJ22
Organism:	Peptoclostridium difficile
Reign:	Bacteria
TaxID:	645463
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	77.186
Number of residues:	34
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.379	513.000

% Hydrophobic	% Polar
44.74	55.26
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	64.52 %
Polar Surface area:	319.88 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-16.7242	-19.4569	46.0959

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
C1'	CG2	ILE- 117	4.17	0	Hydrophobic	false
C5'	CG2	ILE- 117	3.88	0	Hydrophobic	false
C1'	CG	GLU- 160	4.19	0	Hydrophobic	false
O3G	N	GLY- 168	2.89	132.21	H-Bond (Protein Donor)	false
O2G	N	GLY- 170	2.85	165.38	H-Bond (Protein Donor)	false
O1G	N	ARG- 171	3.11	151.94	H-Bond (Protein Donor)	false
O1G	NE	ARG- 171	3.02	146.67	H-Bond (Protein Donor)	false
O3G	NH2	ARG- 171	3.06	145.73	H-Bond (Protein Donor)	false
O1G	CZ	ARG- 171	3.86	0	Ionic (Protein Cationic)	false
O3G	CZ	ARG- 171	3.88	0	Ionic (Protein Cationic)	false
O3'	NH1	ARG- 174	3.35	159.79	H-Bond (Protein Donor)	false
C2'	CE2	TYR- 199	4.05	0	Hydrophobic	false
O2'	OH	TYR- 199	2.57	139.26	H-Bond (Ligand Donor)	false
O1A	CZ	ARG- 200	3.47	0	Ionic (Protein Cationic)	false
C2'	CD1	LEU- 203	3.62	0	Hydrophobic	false
N6	OD1	ASN- 204	3	125.79	H-Bond (Ligand Donor)	false
O3G	MG	MG- 301	2.5	0	Metal Acceptor	false
O1B	MG	MG- 301	2.39	0	Metal Acceptor	false
O2B	MG	MG- 301	2.49	0	Metal Acceptor	false