scPDB - 4dpy entry

Protein Data Bank Entry:

PDB ID : 4dpy

Resolution :2.140 Å

Experimental Method : X-ray

Deposition Date : 2012-02-14

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:	19.970
Number of residues:	35
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.843	482.625

% Hydrophobic	% Polar
48.95	51.05
According to VolSite

Ligand :

HET Code:	2P0
Formula:	C7H9NO10P2
Molecular weight:	329.095 g/mol
DrugBank ID:	-
Buried Surface Area:	75.37 %
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
-15.9226	-30.478	-19.8883

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	4.36	0	Hydrophobic	false
CB	CD	LYS- 17	3.64	0	Hydrophobic	false
O	N	TYR- 18	3.49	144.15	H-Bond (Protein Donor)	false
OAC	OH	TYR- 18	2.68	160.34	H-Bond (Protein Donor)	false
CAK	CD2	TYR- 18	3.94	0	Hydrophobic	false
CG	CE3	TRP- 19	4.26	0	Hydrophobic	false
OAC	NZ	LYS- 21	3.5	0	Ionic (Protein Cationic)	false
OAF	NZ	LYS- 21	2.61	0	Ionic (Protein Cationic)	false
OAF	NZ	LYS- 21	2.61	164.91	H-Bond (Protein Donor)	false
OAG	OG	SER- 139	2.95	165.29	H-Bond (Protein Donor)	false
OAC	N	GLY- 140	2.91	149.09	H-Bond (Protein Donor)	false
OAH	OG	SER- 141	2.75	156.87	H-Bond (Protein Donor)	false
OAH	N	SER- 141	2.97	160.01	H-Bond (Protein Donor)	false
O	NH2	ARG- 144	2.96	141.12	H-Bond (Protein Donor)	false
O	NH1	ARG- 144	3.12	134.84	H-Bond (Protein Donor)	false
OXT	NH2	ARG- 144	3.13	150.69	H-Bond (Protein Donor)	false
O	CZ	ARG- 144	3.45	0	Ionic (Protein Cationic)	false
CAK	CB	ALA- 192	4.18	0	Hydrophobic	false
OAF	CZ	ARG- 193	3.64	0	Ionic (Protein Cationic)	false
OAG	CZ	ARG- 193	3.77	0	Ionic (Protein Cationic)	false
OAF	NE	ARG- 193	2.82	160.07	H-Bond (Protein Donor)	false
OAG	NH2	ARG- 193	2.94	168.17	H-Bond (Protein Donor)	false
CAK	CE	MET- 196	3.98	0	Hydrophobic	false
CG	SD	MET- 243	3.86	0	Hydrophobic	false
CG	CB	ASP- 283	4.09	0	Hydrophobic	false
OXT	O	HOH- 570	3.07	151.04	H-Bond (Protein Donor)	false