scPDB - 4b6s entry

Protein Data Bank Entry:

PDB ID : 4b6s

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2012-08-14

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
B	18 %
C	82 %

Ligand binding site composition:

B-Factor:	27.750
Number of residues:	35
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.286	378.000

% Hydrophobic	% Polar
45.54	54.46
According to VolSite

Ligand :

HET Code:	2HN
Formula:	C14H10F5O6
Molecular weight:	369.218 g/mol
DrugBank ID:	-
Buried Surface Area:	84.94 %
Polar Surface area:	117.89 Å2

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

Mass center Coordinates

X	Y	Z
1.7482	35.6949	-23.9306

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
FAG	CB	ASN- 10	3.65	0	Hydrophobic	false
FAI	CD1	LEU- 11	4.38	0	Hydrophobic	false
CAX	CD2	LEU- 11	4.39	0	Hydrophobic	false
FAK	CD1	LEU- 11	3.38	0	Hydrophobic	false
FAG	CB	MET- 13	3.77	0	Hydrophobic	false
FAI	CG	LEU- 14	3.21	0	Hydrophobic	false
FAK	CD2	LEU- 14	3.84	0	Hydrophobic	false
FAK	CD1	TYR- 22	3.76	0	Hydrophobic	false
FAH	CE2	TYR- 22	4.4	0	Hydrophobic	false
FAJ	CZ	TYR- 22	3.73	0	Hydrophobic	false
CAL	CE1	TYR- 22	3.31	0	Hydrophobic	false
DuAr	DuAr	TYR- 22	3.87	0	Aromatic Face/Face	false
OAF	OD1	ASN- 76	2.83	140.29	H-Bond (Ligand Donor)	false
OAC	ND2	ASN- 76	2.89	157.69	H-Bond (Protein Donor)	false
CAW	CB	ALA- 79	4.5	0	Hydrophobic	false
OAD	NE2	HIS- 82	2.89	165.75	H-Bond (Ligand Donor)	false
FAH	CB	ASP- 89	3.7	0	Hydrophobic	false
FAJ	CB	ASP- 89	4.07	0	Hydrophobic	false
OAE	OD2	ASP- 89	2.55	152.61	H-Bond (Ligand Donor)	false
FAH	CD2	LEU- 93	3.6	0	Hydrophobic	false
FAK	CG	LEU- 103	4.34	0	Hydrophobic	false
CAT	CD1	LEU- 103	4.45	0	Hydrophobic	false
OAC	N	LEU- 103	2.91	155.35	H-Bond (Protein Donor)	false
OAA	N	THR- 104	2.95	163.56	H-Bond (Protein Donor)	false
OAA	OG1	THR- 104	2.86	176.41	H-Bond (Protein Donor)	false
CAM	CG2	ILE- 106	4.02	0	Hydrophobic	false
OAD	NH1	ARG- 113	3.09	155.46	H-Bond (Protein Donor)	false
OAB	O	HOH- 2047	2.89	153.89	H-Bond (Protein Donor)	false