scPDB - 5brp entry

Protein Data Bank Entry:

PDB ID : 5brp

Resolution :2.050 Å

Experimental Method : X-ray

Deposition Date : 2015-06-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glycoside Hydrolase Family 13
ID:	Q65MI2_BACLD
AC:	Q65MI2
Organism:	Bacillus licheniformis
Reign:	Bacteria
TaxID:	279010
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	31.315
Number of residues:	28
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.641	1262.250

% Hydrophobic	% Polar
34.76	65.24
According to VolSite

Ligand :

HET Code:	PNG
Formula:	C12H15NO8
Molecular weight:	301.249 g/mol
DrugBank ID:	-
Buried Surface Area:	60.67 %
Polar Surface area:	145.19 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	4
Rings:	2
Aromatic rings:	1
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
75.194	-62.8401	-61.0305

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
C6	CD2	TYR- 66	4.41	0	Hydrophobic	false
O6	NE2	HIS- 106	3.46	124.3	H-Bond (Protein Donor)	false
C1	CE2	TYR- 167	3.47	0	Hydrophobic	false
C5	CE2	TYR- 167	4.42	0	Hydrophobic	false
C6	CG2	VAL- 204	3.72	0	Hydrophobic	false
C2	CG1	VAL- 204	4.17	0	Hydrophobic	false
C4	CG1	VAL- 204	3.88	0	Hydrophobic	false
O3	OE1	GLU- 254	2.83	127.7	H-Bond (Ligand Donor)	false
O3	OE2	GLU- 254	3.16	163.16	H-Bond (Ligand Donor)	false
N1	O	HOH- 709	3.18	123.71	H-Bond (Protein Donor)	false