scPDB - 2x3f entry

Protein Data Bank Entry:

PDB ID : 2x3f

Resolution :1.950 Å

Experimental Method : X-ray

Deposition Date : 2010-01-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Pantothenate synthetase
ID:	PANC_STAAR
AC:	Q6GDK5
Organism:	Staphylococcus aureus
Reign:	Bacteria
TaxID:	282458
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	26.778
Number of residues:	37
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.150	975.375

% Hydrophobic	% Polar
35.29	64.71
According to VolSite

Ligand :

HET Code:	APC
Formula:	C11H14N5O12P3
Molecular weight:	501.176 g/mol
DrugBank ID:	DB02596
Buried Surface Area:	73.64 %
Polar Surface area:	310.64 Å2

Number of
H-Bond Acceptors:	16
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
17.0714	39.7687	76.0777

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
C5'	CB	THR- 30	4.09	0	Hydrophobic	false
O2A	N	MET- 31	3.02	166.73	H-Bond (Protein Donor)	false
C3A	CE	MET- 31	4.41	0	Hydrophobic	false
O2G	NE2	HIS- 35	3.23	171.07	H-Bond (Protein Donor)	false
O2B	NE2	HIS- 38	2.83	134.74	H-Bond (Protein Donor)	false
C1'	CE	MET- 41	3.63	0	Hydrophobic	false
C4'	CE	MET- 41	3.73	0	Hydrophobic	false
O2A	OH	TYR- 72	3.39	124.25	H-Bond (Protein Donor)	false
C3A	CZ	TYR- 72	4.33	0	Hydrophobic	false
O3'	N	GLY- 148	2.96	174.33	H-Bond (Protein Donor)	false
O3G	NZ	LYS- 150	3.07	137.99	H-Bond (Protein Donor)	false
O3G	NZ	LYS- 150	3.07	0	Ionic (Protein Cationic)	false
O1B	NZ	LYS- 150	3.98	0	Ionic (Protein Cationic)	false
O2'	OD1	ASP- 151	2.77	154.77	H-Bond (Ligand Donor)	false
N6	O	VAL- 177	3.12	164.5	H-Bond (Ligand Donor)	false
N1	N	VAL- 177	2.81	171.88	H-Bond (Protein Donor)	false
N6	O	LYS- 185	2.99	163.25	H-Bond (Ligand Donor)	false
O3G	OG	SER- 186	2.63	160.57	H-Bond (Protein Donor)	false
O1G	N	SER- 187	2.68	171.5	H-Bond (Protein Donor)	false
O3G	CZ	ARG- 188	3.97	0	Ionic (Protein Cationic)	false
O3G	NH1	ARG- 188	2.82	144.18	H-Bond (Protein Donor)	false
O3'	O	HOH- 2014	2.94	176.27	H-Bond (Ligand Donor)	false