scPDB - 4b6r entry

Protein Data Bank Entry:

PDB ID : 4b6r

Resolution :2.000 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
A	88 %
C	12 %

Ligand binding site composition:

B-Factor:	37.209
Number of residues:	34
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.347	361.125

% Hydrophobic	% Polar
47.66	52.34
According to VolSite

Ligand :

HET Code:	3DQ
Formula:	C15H17O7
Molecular weight:	309.291 g/mol
DrugBank ID:	-
Buried Surface Area:	76.67 %
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
23.964	48.7236	-14.249

Binding mode :

What is Poseview ?

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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	4.26	0	Hydrophobic	false
CAH	CD2	LEU- 11	3.88	0	Hydrophobic	false
CAA	CB	MET- 13	4.24	0	Hydrophobic	false
CAJ	CD2	LEU- 14	4	0	Hydrophobic	false
CAL	CZ	TYR- 22	3.67	0	Hydrophobic	false
DuAr	DuAr	TYR- 22	3.84	0	Aromatic Edge/Face	false
OAD	ND2	ASN- 76	2.9	160.71	H-Bond (Protein Donor)	false
OAG	OD1	ASN- 76	2.93	139.17	H-Bond (Ligand Donor)	false
OAE	NE2	HIS- 82	2.81	174.93	H-Bond (Ligand Donor)	false
OAF	OD2	ASP- 89	2.61	143.38	H-Bond (Ligand Donor)	false
CAA	CD2	LEU- 93	3.84	0	Hydrophobic	false
CAR	CD2	LEU- 93	4.35	0	Hydrophobic	false
CAH	CD1	LEU- 103	4.32	0	Hydrophobic	false
OAD	N	LEU- 103	2.86	149.86	H-Bond (Protein Donor)	false
OAB	OG1	THR- 104	2.72	174.93	H-Bond (Protein Donor)	false
OAB	N	THR- 104	2.76	162.09	H-Bond (Protein Donor)	false
CAM	CG2	ILE- 106	3.93	0	Hydrophobic	false
CAS	CD	ARG- 113	4.4	0	Hydrophobic	false
OAE	NH1	ARG- 113	2.88	156.3	H-Bond (Protein Donor)	false
OAC	O	HOH- 2004	2.88	179.97	H-Bond (Protein Donor)	false