scPDB - 4e8y entry

Protein Data Bank Entry:

PDB ID : 4e8y

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2012-03-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	D-beta-D-heptose 7-phosphate kinase
ID:	B4EB35_BURCJ
AC:	B4EB35
Organism:	Burkholderia cenocepacia )
Reign:	Bacteria
TaxID:	216591
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	43.913
Number of residues:	33
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.907	479.250

% Hydrophobic	% Polar
51.41	48.59
According to VolSite

Ligand :

HET Code:	IHA
Formula:	C21H18N5O5S
Molecular weight:	452.463 g/mol
DrugBank ID:	-
Buried Surface Area:	59.24 %
Polar Surface area:	159.65 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	1
Rings:	4
Aromatic rings:	4
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
13.2767	-12.1553	32.1032

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
C22	CB	ASN- 202	4.38	0	Hydrophobic	false
S31	CG2	THR- 238	4.24	0	Hydrophobic	false
C30	CB	THR- 238	3.49	0	Hydrophobic	false
C21	CB	SER- 240	4.47	0	Hydrophobic	false
C6	CB	SER- 240	3.48	0	Hydrophobic	false
N19	N	SER- 240	2.89	131	H-Bond (Protein Donor)	false
C1	CB	GLU- 241	4.11	0	Hydrophobic	false
C4	CG	GLU- 241	4.32	0	Hydrophobic	false
S31	SD	MET- 244	4.46	0	Hydrophobic	false
C17	CG	MET- 244	4.1	0	Hydrophobic	false
N13	N	ALA- 259	3.34	146.46	H-Bond (Protein Donor)	false
C1	CG2	VAL- 262	3.88	0	Hydrophobic	false
C3	CG2	VAL- 262	3.46	0	Hydrophobic	false
C24	CG1	VAL- 265	4.12	0	Hydrophobic	false
C9	CG1	VAL- 265	3.46	0	Hydrophobic	false
C6	CG1	VAL- 265	4.44	0	Hydrophobic	false
C9	CB	ALA- 268	4.11	0	Hydrophobic	false
C29	CB	ALA- 268	3.66	0	Hydrophobic	false
S31	CG2	VAL- 272	3.86	0	Hydrophobic	false
C29	CG2	VAL- 272	3.98	0	Hydrophobic	false
S31	CB	ALA- 297	3.57	0	Hydrophobic	false
C7	CG1	VAL- 301	4.32	0	Hydrophobic	false
C9	CG1	VAL- 301	3.97	0	Hydrophobic	false