scPDB - 2zx9 entry

Protein Data Bank Entry:

PDB ID : 2zx9

Resolution :2.620 Å

Experimental Method : X-ray

Deposition Date : 2008-12-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Alpha-L-fucosidase, putative
ID:	Q9WYE2_THEMA
AC:	Q9WYE2
Organism:	Thermotoga maritima
Reign:	Bacteria
TaxID:	243274
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	30.071
Number of residues:	30
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.281	475.875

% Hydrophobic	% Polar
45.39	54.61
According to VolSite

Ligand :

HET Code:	ZX9
Formula:	C20H31N2O4
Molecular weight:	363.471 g/mol
DrugBank ID:	-
Buried Surface Area:	61.15 %
Polar Surface area:	106.4 Å2

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

Mass center Coordinates

X	Y	Z
26.4174	4.07719	55.83

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
CAA	CE2	PHE- 32	3.95	0	Hydrophobic	false
OAC	NE2	HIS- 34	2.76	143.56	H-Bond (Ligand Donor)	false
CAZ	CD2	LEU- 50	4.37	0	Hydrophobic	false
CAM	CD2	LEU- 50	3.68	0	Hydrophobic	false
CAK	CD1	LEU- 50	4.27	0	Hydrophobic	false
CAK	CE	MET- 55	3.56	0	Hydrophobic	false
CAV	CD2	TYR- 64	3.7	0	Hydrophobic	false
CAW	CE2	TYR- 64	4.49	0	Hydrophobic	false
OAD	OE1	GLU- 66	2.66	170.3	H-Bond (Ligand Donor)	false
OAD	NE1	TRP- 67	3.35	126.68	H-Bond (Protein Donor)	false
OAE	NE1	TRP- 67	2.61	154	H-Bond (Protein Donor)	false
OAC	NE2	HIS- 128	2.81	159.84	H-Bond (Protein Donor)	false
OAE	NE2	HIS- 129	2.71	157.32	H-Bond (Ligand Donor)	false
CAL	CD1	LEU- 191	3.97	0	Hydrophobic	false
NAQ	OD2	ASP- 224	3.92	0	Ionic (Ligand Cationic)	false
NAQ	OD1	ASP- 224	2.67	0	Ionic (Ligand Cationic)	false
NAQ	OD1	ASP- 224	2.67	154.74	H-Bond (Ligand Donor)	false
CAI	CB	GLU- 266	4.37	0	Hydrophobic	false
NAP	OE1	GLU- 266	3.4	123.11	H-Bond (Ligand Donor)	false
NAQ	OE2	GLU- 266	3.03	149.51	H-Bond (Ligand Donor)	false
NAQ	OE2	GLU- 266	3.03	0	Ionic (Ligand Cationic)	false
NAQ	OE1	GLU- 266	3.6	0	Ionic (Ligand Cationic)	false
CAF	CG1	VAL- 269	3.41	0	Hydrophobic	false
CAA	CG2	THR- 283	4.41	0	Hydrophobic	false
CAA	CZ	PHE- 290	3.49	0	Hydrophobic	false
CAU	CD1	PHE- 290	3.98	0	Hydrophobic	false