scPDB - 2xda entry

Protein Data Bank Entry:

PDB ID : 2xda

Resolution :1.850 Å

Experimental Method : X-ray

Deposition Date : 2010-04-30

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	100 %

Ligand binding site composition:

B-Factor:	20.481
Number of residues:	33
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.513	313.875

% Hydrophobic	% Polar
48.39	51.61
According to VolSite

Ligand :

HET Code:	JPS
Formula:	C14H17O5S
Molecular weight:	297.347 g/mol
DrugBank ID:	-
Buried Surface Area:	79.1 %
Polar Surface area:	129.06 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	3
Rings:	3
Aromatic rings:	1
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
1.63205	14.0931	24.0379

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
CAH	CB	ASN- 10	4.3	0	Hydrophobic	false
SAK	CB	ASN- 10	4.48	0	Hydrophobic	false
CAH	CD2	LEU- 11	3.89	0	Hydrophobic	false
CA1	CB	MET- 13	3.61	0	Hydrophobic	false
CAA	CD1	LEU- 14	4.06	0	Hydrophobic	false
CA1	CB	ARG- 17	4.48	0	Hydrophobic	false
CAG	CE1	TYR- 22	3.81	0	Hydrophobic	false
CAH	CE2	TYR- 22	4.46	0	Hydrophobic	false
CA0	CD1	TYR- 22	3.44	0	Hydrophobic	false
OAC	ND2	ASN- 76	2.95	158	H-Bond (Protein Donor)	false
OAF	OD1	ASN- 76	2.88	135.08	H-Bond (Ligand Donor)	false
OAD	NE2	HIS- 82	2.76	157.32	H-Bond (Ligand Donor)	false
OAC	N	LEU- 103	2.77	154.82	H-Bond (Protein Donor)	false
OAB	OG1	THR- 104	2.63	178.47	H-Bond (Protein Donor)	false
OAB	N	THR- 104	2.86	161.17	H-Bond (Protein Donor)	false
CAJ	CG2	ILE- 106	3.97	0	Hydrophobic	false
OAD	NH1	ARG- 113	2.86	154.29	H-Bond (Protein Donor)	false
OAE	O	HOH- 2001	3.22	179.94	H-Bond (Protein Donor)	false