scPDB - 2xd6 entry

Protein Data Bank Entry:

PDB ID : 2xd6

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2010-04-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	ATP-dependent molecular chaperone HSP82
ID:	HSP82_YEAST
AC:	P02829
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	18.562
Number of residues:	31
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.090	489.375

% Hydrophobic	% Polar
48.28	51.72
According to VolSite

Ligand :

HET Code:	XD6
Formula:	C18H18ClO6
Molecular weight:	365.785 g/mol
DrugBank ID:	-
Buried Surface Area:	61.81 %
Polar Surface area:	103.73 Å2

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

Mass center Coordinates

X	Y	Z
-16.791	2.88384	-5.18796

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
C5	CB	ASN- 37	3.59	0	Hydrophobic	false
C6	CB	ASN- 37	3.93	0	Hydrophobic	false
C21	CB	ASP- 40	4.23	0	Hydrophobic	false
C17	CB	ALA- 41	4.12	0	Hydrophobic	false
C3	CB	ALA- 41	3.89	0	Hydrophobic	false
C16	CD	LYS- 44	3.82	0	Hydrophobic	false
C21	CD	LYS- 44	3.3	0	Hydrophobic	false
O22	NZ	LYS- 44	3.03	145.44	H-Bond (Protein Donor)	false
O3	OD2	ASP- 79	3.1	125.48	H-Bond (Ligand Donor)	false
C16	CG2	ILE- 82	3.53	0	Hydrophobic	false
C8	SD	MET- 84	3.5	0	Hydrophobic	false
C17	CG	MET- 84	3.93	0	Hydrophobic	false
C7	CE	MET- 84	3.89	0	Hydrophobic	false
C10	CB	ASN- 92	4.04	0	Hydrophobic	false
C10	CD2	LEU- 93	4.3	0	Hydrophobic	false
CL1	CD2	LEU- 93	4.28	0	Hydrophobic	false
CL1	CG	PHE- 124	3.66	0	Hydrophobic	false
C2	CG2	THR- 171	4.4	0	Hydrophobic	false
C3	CB	THR- 171	3.82	0	Hydrophobic	false
C4	CG2	THR- 171	4.22	0	Hydrophobic	false
O2	OG1	THR- 171	2.92	142.32	H-Bond (Protein Donor)	false
C6	CD1	LEU- 173	4.34	0	Hydrophobic	false
C5	CD1	LEU- 173	3.66	0	Hydrophobic	false