scPDB - 2wks entry

Protein Data Bank Entry:

PDB ID : 2wks

Resolution :2.950 Å

Experimental Method : X-ray

Deposition Date : 2009-06-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	6.890	6.890	6.890	0.000	6.890	1

List of CHEMBLId :

CHEMBL567564

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
C	24 %
D	76 %

Ligand binding site composition:

B-Factor:	45.690
Number of residues:	37
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.218	391.500

% Hydrophobic	% Polar
67.24	32.76
According to VolSite

Ligand :

HET Code:	CB6
Formula:	C17H17O6S
Molecular weight:	349.378 g/mol
DrugBank ID:	-
Buried Surface Area:	78.46 %
Polar Surface area:	138.29 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
6.32246	13.7907	24.8051

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
CAT	CB	ASN- 10	4.41	0	Hydrophobic	false
SAO	CB	ASN- 10	4.24	0	Hydrophobic	false
CAL	CB	ASN- 10	4.36	0	Hydrophobic	false
SAO	CD2	LEU- 11	4.32	0	Hydrophobic	false
CAL	CD2	LEU- 11	3.62	0	Hydrophobic	false
SAO	CD2	LEU- 14	3.96	0	Hydrophobic	false
CAR	CB	PRO- 19	4.02	0	Hydrophobic	false
CAJ	CG	PRO- 19	4.5	0	Hydrophobic	false
SAO	CD2	TYR- 22	3.95	0	Hydrophobic	false
CAL	CE2	TYR- 22	3.64	0	Hydrophobic	false
CAW	CE2	TYR- 22	4.03	0	Hydrophobic	false
CAT	CE1	TYR- 22	3.33	0	Hydrophobic	false
CAX	CE2	TYR- 22	4.36	0	Hydrophobic	false
OAC	ND2	ASN- 76	2.83	150.36	H-Bond (Protein Donor)	false
OAF	OD1	ASN- 76	2.81	145.48	H-Bond (Ligand Donor)	false
OAD	NE2	HIS- 82	2.84	150.33	H-Bond (Ligand Donor)	false
CAI	CB	ASP- 89	4.22	0	Hydrophobic	false
CAA	CB	MET- 92	3.96	0	Hydrophobic	false
CAA	CB	LEU- 93	3.47	0	Hydrophobic	false
CAR	CD2	LEU- 93	3.36	0	Hydrophobic	false
CAX	CB	HIS- 102	4.43	0	Hydrophobic	false
OAC	N	LEU- 103	2.69	146.8	H-Bond (Protein Donor)	false
OAB	OG1	THR- 104	2.69	173.82	H-Bond (Protein Donor)	false
OAB	N	THR- 104	2.96	165.05	H-Bond (Protein Donor)	false
CAM	CG2	ILE- 106	3.92	0	Hydrophobic	false
OAD	NH1	ARG- 113	2.65	136.07	H-Bond (Protein Donor)	false
OAE	NH1	ARG- 113	3.01	132.5	H-Bond (Protein Donor)	false