scPDB - 2xb8 entry

Protein Data Bank Entry:

PDB ID : 2xb8

Resolution :2.400 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_MYCTU
AC:	P9WPX7
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	4.2.1.10

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	20.422
Number of residues:	28
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.183	313.875

% Hydrophobic	% Polar
51.61	48.39
According to VolSite

Ligand :

HET Code:	XNW
Formula:	C15H17O7
Molecular weight:	309.291 g/mol
DrugBank ID:	-
Buried Surface Area:	75.12 %
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
14.2355	2.58882	38.5406

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
CAJ	CB	ASN- 12	3.65	0	Hydrophobic	false
CAH	CG	LEU- 13	4.32	0	Hydrophobic	false
CAL	CG	LEU- 13	3.88	0	Hydrophobic	false
CAI	CD2	LEU- 13	3.63	0	Hydrophobic	false
CAA	CB	ARG- 15	3.7	0	Hydrophobic	false
CAK	CD1	LEU- 16	3.38	0	Hydrophobic	false
CAA	CD2	TYR- 24	4.32	0	Hydrophobic	false
CAK	CB	TYR- 24	3.86	0	Hydrophobic	false
CAU	CE1	TYR- 24	3.91	0	Hydrophobic	false
DuAr	DuAr	TYR- 24	3.69	0	Aromatic Face/Face	false
OAB	ND2	ASN- 75	2.8	142.69	H-Bond (Protein Donor)	false
OAG	OD1	ASN- 75	2.67	130.64	H-Bond (Ligand Donor)	false
OAE	NE2	HIS- 81	2.7	164.09	H-Bond (Ligand Donor)	false
CAV	CB	HIS- 101	4.37	0	Hydrophobic	false
CAI	CD1	ILE- 102	4.38	0	Hydrophobic	false
OAB	N	ILE- 102	2.79	160.92	H-Bond (Protein Donor)	false
OAD	N	SER- 103	3.01	162.22	H-Bond (Protein Donor)	false
OAD	OG	SER- 103	2.74	163.02	H-Bond (Protein Donor)	false
CAM	CG1	VAL- 105	3.72	0	Hydrophobic	false
OAE	NH1	ARG- 112	2.92	150.34	H-Bond (Protein Donor)	false