scPDB - 4dpt entry

Protein Data Bank Entry:

PDB ID : 4dpt

Resolution :2.190 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
B	100 %

Ligand binding site composition:

B-Factor:	43.971
Number of residues:	41
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.129	482.625

% Hydrophobic	% Polar
39.16	60.84
According to VolSite

Ligand :

HET Code:	AGS
Formula:	C10H14N5O12P3S
Molecular weight:	521.231 g/mol
DrugBank ID:	DB02930
Buried Surface Area:	56.82 %
Polar Surface area:	329.24 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
10.4225	14.6143	13.3735

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
N6	OG	SER- 94	2.64	157.86	H-Bond (Ligand Donor)	false
N7	ND2	ASN- 96	2.98	159.35	H-Bond (Protein Donor)	false
N6	OD1	ASN- 96	3.42	166.18	H-Bond (Ligand Donor)	false
C5'	CB	ALA- 101	4.13	0	Hydrophobic	false
C3'	CB	ALA- 101	4.47	0	Hydrophobic	false
O2B	N	ALA- 105	2.92	131.51	H-Bond (Protein Donor)	false
O1B	OG	SER- 106	2.61	133.86	H-Bond (Protein Donor)	false
O1B	N	SER- 106	2.86	135.8	H-Bond (Protein Donor)	false
O2G	N	SER- 107	3.22	124.96	H-Bond (Protein Donor)	false
O1B	N	SER- 107	3.33	128.33	H-Bond (Protein Donor)	false
O3B	N	SER- 107	3.2	143	H-Bond (Protein Donor)	false
C5'	CB	SER- 107	3.55	0	Hydrophobic	false
O2G	N	ALA- 108	3.01	143.03	H-Bond (Protein Donor)	false
O1A	OG	SER- 192	3	163.69	H-Bond (Protein Donor)	false
O1A	N	SER- 192	3.24	155.81	H-Bond (Protein Donor)	false