scPDB - 3ryk entry

Protein Data Bank Entry:

PDB ID : 3ryk

Resolution :1.630 Å

Experimental Method : X-ray

Deposition Date : 2011-05-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	dTDP-4-dehydrorhamnose 3,5-epimerase
ID:	Q81TP1_BACAN
AC:	Q81TP1
Organism:	Bacillus anthracis
Reign:	Bacteria
TaxID:	1392
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	27 %
B	73 %

Ligand binding site composition:

B-Factor:	30.254
Number of residues:	24
Including
Standard Amino Acids:	22
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.346	523.125

% Hydrophobic	% Polar
43.23	56.77
According to VolSite

Ligand :

HET Code:	TYD
Formula:	C10H13N2O11P2
Molecular weight:	399.165 g/mol
DrugBank ID:	DB03103
Buried Surface Area:	34.79 %
Polar Surface area:	220.27 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	2
Rings:	2
Aromatic rings:	0
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
4.85368	22.755	-39.4728

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
C5'	CB	PHE- 26	4.33	0	Hydrophobic	false
C4'	CD2	PHE- 26	4.46	0	Hydrophobic	false
C1'	CE2	PHE- 26	4.02	0	Hydrophobic	false
C5M	CZ	PHE- 26	4.06	0	Hydrophobic	false
N3	OE2	GLU- 28	2.84	157.59	H-Bond (Ligand Donor)	false
O4	ND2	ASN- 48	3.24	122.25	H-Bond (Protein Donor)	false
C2'	CZ	TYR- 138	4.17	0	Hydrophobic	false
C5M	CD1	TYR- 138	3.61	0	Hydrophobic	false
O3B	OG	SER- 165	2.87	148.4	H-Bond (Protein Donor)	false