scPDB - 2xb9 entry

Protein Data Bank Entry:

PDB ID : 2xb9

Resolution :2.750 Å

Experimental Method : X-ray

Deposition Date : 2010-04-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	3-dehydroquinate dehydratase
ID:	AROQ_HELPY
AC:	Q48255
Organism:	Helicobacter pylori
Reign:	Bacteria
TaxID:	85962
EC Number:	4.2.1.10

Chains:

Chain Name:	Percentage of Residues within binding site
A	87 %
C	13 %

Ligand binding site composition:

B-Factor:	37.686
Number of residues:	32
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.619	357.750

% Hydrophobic	% Polar
52.83	47.17
According to VolSite

Ligand :

HET Code:	XNW
Formula:	C15H17O7
Molecular weight:	309.291 g/mol
DrugBank ID:	-
Buried Surface Area:	79.72 %
Polar Surface area:	127.12 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	3
Rings:	2
Aromatic rings:	1
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
-24.1883	48.7446	14.2321

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
CAK	CB	ASN- 10	3.43	0	Hydrophobic	false
CAI	CG	LEU- 11	4.37	0	Hydrophobic	false
CAL	CD2	LEU- 11	3.78	0	Hydrophobic	false
CAQ	CD2	LEU- 11	4.03	0	Hydrophobic	false
CAJ	CD1	LEU- 14	3.77	0	Hydrophobic	false
CAA	CD2	TYR- 22	3.67	0	Hydrophobic	false
CAL	CE1	TYR- 22	4.06	0	Hydrophobic	false
DuAr	DuAr	TYR- 22	3.96	0	Aromatic Edge/Face	false
OAB	ND2	ASN- 76	3.04	143.83	H-Bond (Protein Donor)	false
OAE	NE2	HIS- 82	2.63	173.47	H-Bond (Protein Donor)	false
OAF	OD2	ASP- 89	2.83	134.26	H-Bond (Ligand Donor)	false
CAA	CD2	LEU- 93	3.77	0	Hydrophobic	false
CAR	CD2	LEU- 93	4.05	0	Hydrophobic	false
OAG	ND1	HIS- 102	3.32	166.27	H-Bond (Ligand Donor)	false
CAH	CD1	LEU- 103	4.3	0	Hydrophobic	false
OAB	N	LEU- 103	2.75	141.46	H-Bond (Protein Donor)	false
OAD	N	THR- 104	2.82	146.84	H-Bond (Protein Donor)	false
OAD	OG1	THR- 104	2.58	159.82	H-Bond (Protein Donor)	false
CAM	CG2	ILE- 106	3.87	0	Hydrophobic	false
OAE	NH1	ARG- 113	3.22	157.55	H-Bond (Protein Donor)	false
OAC	O	HOH- 2010	2.77	179.97	H-Bond (Protein Donor)	false