scPDB - 5bv3 entry

Protein Data Bank Entry:

PDB ID : 5bv3

Resolution :2.250 Å

Experimental Method : X-ray

Deposition Date : 2015-06-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	m7GpppX diphosphatase
ID:	DCPS_YEAST
AC:	Q06151
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	3.6.1.59

Chains:

Chain Name:	Percentage of Residues within binding site
C	82 %
D	18 %

Ligand binding site composition:

B-Factor:	47.323
Number of residues:	33
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.401	2031.750

% Hydrophobic	% Polar
46.18	53.82
According to VolSite

Ligand :

HET Code:	M7G
Formula:	C11H16N5O11P2
Molecular weight:	456.219 g/mol
DrugBank ID:	DB01960
Buried Surface Area:	79.88 %
Polar Surface area:	265.04 Å2

Number of
H-Bond Acceptors:	15
H-Bond Donors:	4
Rings:	3
Aromatic rings:	0
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
27.878	-19.2763	87.5091

Binding mode :

What is Poseview ?

2D View
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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
CM7	CE2	TYR- 94	3.23	0	Hydrophobic	false
O3B	NZ	LYS- 126	3.32	156.59	H-Bond (Protein Donor)	false
O3B	NZ	LYS- 126	3.32	0	Ionic (Protein Cationic)	false
C1'	CH2	TRP- 161	4.21	0	Hydrophobic	false
C8	CZ2	TRP- 161	3.55	0	Hydrophobic	false
CM7	CD2	TRP- 161	3.73	0	Hydrophobic	false
N1	OE1	GLU- 171	2.86	166.09	H-Bond (Ligand Donor)	false
N2	OE2	GLU- 171	3.04	163.8	H-Bond (Ligand Donor)	false
N2	O	PRO- 193	2.9	124.98	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 194	2.55	155.24	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 194	3.06	130.75	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 194	2.6	147.16	H-Bond (Ligand Donor)	false
C1'	CB	MET- 195	4.41	0	Hydrophobic	false
C8	CE	MET- 195	3.72	0	Hydrophobic	false
CM7	CE	MET- 195	3.76	0	Hydrophobic	false
N3	N	MET- 195	3.24	158.89	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 196	3	143.23	H-Bond (Protein Donor)	false
O2'	NZ	LYS- 196	3.44	168.76	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 196	3	0	Ionic (Protein Cationic)	false
C4'	CG2	VAL- 208	4.48	0	Hydrophobic	false
O2A	N	SER- 263	2.92	122.46	H-Bond (Protein Donor)	false
O1B	N	SER- 263	3.46	140.52	H-Bond (Protein Donor)	false
O1B	OG	SER- 263	3.5	126.54	H-Bond (Protein Donor)	false
O3B	OG	SER- 263	2.79	162.35	H-Bond (Protein Donor)	false
O2A	N	TYR- 264	3.1	152.2	H-Bond (Protein Donor)	false
C5'	CD2	TYR- 264	4.19	0	Hydrophobic	false
C8	CE2	TYR- 264	3.94	0	Hydrophobic	false
CM7	CZ	TYR- 264	4.44	0	Hydrophobic	false
O1A	NE2	HIS- 270	3.01	137.09	H-Bond (Protein Donor)	false
O5'	NE2	HIS- 270	2.93	133	H-Bond (Protein Donor)	false