scPDB - 3n2e entry

Protein Data Bank Entry:

PDB ID : 3n2e

Resolution :2.530 Å

Experimental Method : X-ray

Deposition Date : 2010-05-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Shikimate kinase
ID:	AROK_HELPY
AC:	P56073
Organism:	Helicobacter pylori
Reign:	Bacteria
TaxID:	85962
EC Number:	2.7.1.71

Chains:

Chain Name:	Percentage of Residues within binding site
A	3 %
B	97 %

Ligand binding site composition:

B-Factor:	40.915
Number of residues:	34
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.641	1822.500

% Hydrophobic	% Polar
48.15	51.85
According to VolSite

Ligand :

HET Code:	OSA
Formula:	C20H13N3O8S2
Molecular weight:	487.463 g/mol
DrugBank ID:	-
Buried Surface Area:	59.22 %
Polar Surface area:	222.35 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	3
Rings:	4
Aromatic rings:	4
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
68.1437	12.1181	9.95985

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
OBE	N	MET- 10	3.16	167.83	H-Bond (Protein Donor)	false
DuAr	DuAr	PHE- 48	3.99	0	Aromatic Face/Face	false
CAR	CE1	PHE- 48	3.47	0	Hydrophobic	false
CAW	CB	PHE- 48	3.99	0	Hydrophobic	false
CAF	CG2	VAL- 83	3.98	0	Hydrophobic	false
CAB	CE	MET- 84	3.34	0	Hydrophobic	false
OBG	NH1	ARG- 116	3.13	148.56	H-Bond (Protein Donor)	false
OBG	NH2	ARG- 116	3.13	147.76	H-Bond (Protein Donor)	false
OBG	CZ	ARG- 116	3.56	0	Ionic (Protein Cationic)	false
DuAr	CZ	ARG- 116	3.72	156.12	Pi/Cation	false
CAS	CD	ARG- 116	3.67	0	Hydrophobic	false
CAS	CD	ARG- 116	3.67	0	Hydrophobic	false
CAE	CB	ARG- 132	3.45	0	Hydrophobic	false
CAF	CG	ARG- 132	3.26	0	Hydrophobic	false
CAD	CD	ARG- 132	3.28	0	Hydrophobic	false
DuAr	CZ	ARG- 132	3.9	150.75	Pi/Cation	false
DuAr	CZ	ARG- 132	3.84	27.53	Pi/Cation	false
CAF	CD2	LEU- 135	4.48	0	Hydrophobic	false
OBF	O	HOH- 187	2.92	159.91	H-Bond (Protein Donor)	false