scPDB - 4du8 entry

Protein Data Bank Entry:

PDB ID : 4du8

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2012-02-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Mevalonate diphosphate decarboxylase
ID:	Q9FD73_STAEP
AC:	Q9FD73
Organism:	Staphylococcus epidermidis
Reign:	Bacteria
TaxID:	1282
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	23.325
Number of residues:	34
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.964	847.125

% Hydrophobic	% Polar
40.24	59.76
According to VolSite

Ligand :

HET Code:	2P0
Formula:	C7H9NO10P2
Molecular weight:	329.095 g/mol
DrugBank ID:	-
Buried Surface Area:	73.47 %
Polar Surface area:	201.84 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	0
Rings:	1
Aromatic rings:	0
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
15.8934	20.5094	19.732

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
CB	CB	ALA- 14	3.96	0	Hydrophobic	false
CG	CD	LYS- 17	3.47	0	Hydrophobic	false
CAK	CE2	TYR- 18	3.71	0	Hydrophobic	false
CG	CE3	TRP- 19	4.44	0	Hydrophobic	false
OAF	NZ	LYS- 21	2.73	162.5	H-Bond (Protein Donor)	false
OAF	NZ	LYS- 21	2.73	0	Ionic (Protein Cationic)	false
OAG	NZ	LYS- 21	3.41	0	Ionic (Protein Cationic)	false
OAH	OG	SER- 107	3.21	145.4	H-Bond (Protein Donor)	false
OAC	OG	SER- 139	2.73	156.62	H-Bond (Protein Donor)	false
OAG	N	GLY- 140	3.07	143.82	H-Bond (Protein Donor)	false
OAD	N	SER- 141	3.01	161.06	H-Bond (Protein Donor)	false
OAD	OG	SER- 141	2.98	153.59	H-Bond (Protein Donor)	false
O	NH2	ARG- 144	3.14	161.92	H-Bond (Protein Donor)	false
OXT	NH1	ARG- 144	2.85	140.72	H-Bond (Protein Donor)	false
OXT	NH2	ARG- 144	2.95	136.22	H-Bond (Protein Donor)	false
OXT	CZ	ARG- 144	3.3	0	Ionic (Protein Cationic)	false
OAM	OG	SER- 192	3.25	174.44	H-Bond (Protein Donor)	false
OAC	NH2	ARG- 193	3.12	163.21	H-Bond (Protein Donor)	false
OAF	NH2	ARG- 193	3.46	129.79	H-Bond (Protein Donor)	false
OAF	NE	ARG- 193	2.78	169.71	H-Bond (Protein Donor)	false
OAF	CZ	ARG- 193	3.55	0	Ionic (Protein Cationic)	false
CAK	CE	MET- 196	3.87	0	Hydrophobic	false
CG	SD	MET- 243	3.69	0	Hydrophobic	false
CG	CB	ALA- 283	4.26	0	Hydrophobic	false