scPDB - 5c7t entry

Protein Data Bank Entry:

PDB ID : 5c7t

Resolution :2.060 Å

Experimental Method : X-ray

Deposition Date : 2015-06-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	ADP-ribose pyrophosphatase
ID:	Q6MIH8_BDEBA
AC:	Q6MIH8
Organism:	Bdellovibrio bacteriovorus
Reign:	Bacteria
TaxID:	264462
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	70 %
B	30 %

Ligand binding site composition:

B-Factor:	29.000
Number of residues:	46
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	6
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.047	799.875

% Hydrophobic	% Polar
32.07	67.93
According to VolSite

Ligand :

HET Code:	APR
Formula:	C15H21N5O14P2
Molecular weight:	557.300 g/mol
DrugBank ID:	-
Buried Surface Area:	62.31 %
Polar Surface area:	316.8 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	4
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
16.3774	98.3206	17.4452

Binding mode :

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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
N1	N	GLU- 38	3.02	165.8	H-Bond (Protein Donor)	false
O1B	NH1	ARG- 64	2.83	160.34	H-Bond (Protein Donor)	false
O2B	NH2	ARG- 64	2.73	153.25	H-Bond (Protein Donor)	false
O2B	NH1	ARG- 64	3.45	125.85	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 64	3.82	0	Ionic (Protein Cationic)	false
O2B	CZ	ARG- 64	3.51	0	Ionic (Protein Cationic)	false
C5D	CB	ALA- 76	4.32	0	Hydrophobic	false
O1A	N	LYS- 78	2.91	156.43	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 78	3.52	0	Ionic (Protein Cationic)	false
N6	O	GLY- 115	2.68	160.04	H-Bond (Ligand Donor)	false
O2D	N	GLY- 115	3.05	143.73	H-Bond (Protein Donor)	false
O3D	OE1	GLU- 119	3.25	124.3	H-Bond (Ligand Donor)	false
O1D	NZ	LYS- 165	2.67	169.68	H-Bond (Protein Donor)	false
C1D	CD	LYS- 165	3.86	0	Hydrophobic	false
O2B	O	HOH- 321	2.76	153.93	H-Bond (Protein Donor)	false