scPDB - 4i5v entry

Protein Data Bank Entry:

PDB ID : 4i5v

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2012-11-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Diadenosine 5',5'''-P1,P4-tetraphosphate phosphorylase 2
ID:	APA2_YEAST
AC:	P22108
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	69.737
Number of residues:	48
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.181	1447.875

% Hydrophobic	% Polar
45.45	54.55
According to VolSite

Ligand :

HET Code:	B4P
Formula:	C20H24N10O19P4
Molecular weight:	832.355 g/mol
DrugBank ID:	-
Buried Surface Area:	62.86 %
Polar Surface area:	484.53 Å2

Number of
H-Bond Acceptors:	27
H-Bond Donors:	6
Rings:	6
Aromatic rings:	4
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
30.9688	-13.2928	21.2313

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
O1B	NZ	LYS- 53	2.96	0	Ionic (Protein Cationic)	false
C1F	CZ	PHE- 68	4.48	0	Hydrophobic	false
C5F	CZ	PHE- 68	4.21	0	Hydrophobic	false
O3E	ND2	ASN- 92	2.78	126.02	H-Bond (Protein Donor)	false
O2F	OD1	ASN- 92	2.67	154.8	H-Bond (Ligand Donor)	false
N3B	N	LYS- 93	3.25	153.68	H-Bond (Protein Donor)	false
C4E	CG2	VAL- 96	4.21	0	Hydrophobic	false
C1E	CG2	VAL- 96	4.3	0	Hydrophobic	false
C4F	CD2	LEU- 102	4.06	0	Hydrophobic	false
C1F	CD1	LEU- 102	4.43	0	Hydrophobic	false
O1D	ND2	ASN- 148	3.07	153.08	H-Bond (Protein Donor)	false
O1B	OG	SER- 156	3.49	145.55	H-Bond (Protein Donor)	false
O2B	OG	SER- 156	2.54	141.22	H-Bond (Protein Donor)	false
O2D	N	SER- 156	2.98	136.12	H-Bond (Protein Donor)	false
C5F	CB	GLN- 157	4.12	0	Hydrophobic	false
O1G	NE2	GLN- 163	3.16	149.37	H-Bond (Protein Donor)	false
O3F	OE1	GLN- 163	2.75	162.63	H-Bond (Ligand Donor)	false
O2G	ND2	ASN- 277	3.19	169.1	H-Bond (Protein Donor)	false
C5E	CD2	LEU- 286	3.93	0	Hydrophobic	false
O1A	NZ	LYS- 288	3.5	143.94	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 288	3.5	0	Ionic (Protein Cationic)	false
N6A	O	HOH- 514	3.2	146.62	H-Bond (Ligand Donor)	false
N3A	O	HOH- 516	3.11	179.98	H-Bond (Protein Donor)	false