scPDB - 5ify entry

Protein Data Bank Entry:

PDB ID : 5ify

Resolution :2.250 Å

Experimental Method : X-ray

Deposition Date : 2016-02-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glucose-1-phosphate thymidylyltransferase
ID:	A4JC15_BURVG
AC:	A4JC15
Organism:	Burkholderia vietnamiensis )
Reign:	Bacteria
TaxID:	269482
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	42.316
Number of residues:	47
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.522	648.000

% Hydrophobic	% Polar
41.15	58.85
According to VolSite

Ligand :

HET Code:	TRH
Formula:	C16H24N2O15P2
Molecular weight:	546.314 g/mol
DrugBank ID:	DB03723
Buried Surface Area:	69.82 %
Polar Surface area:	276.36 Å2

Number of
H-Bond Acceptors:	15
H-Bond Donors:	5
Rings:	3
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-55.0324	41.4146	-1.97137

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
O21	N	GLY- 10	2.78	129.45	H-Bond (Protein Donor)	false
C2'	CB	SER- 12	3.92	0	Hydrophobic	false
N31	OE1	GLN- 82	2.85	165.44	H-Bond (Ligand Donor)	false
O41	NE2	GLN- 82	2.87	133.74	H-Bond (Protein Donor)	false
C5A	CB	PRO- 85	4.44	0	Hydrophobic	false
O41	N	GLY- 87	2.92	156.72	H-Bond (Protein Donor)	false
C1	CD2	LEU- 88	4.17	0	Hydrophobic	false
C5	CD2	LEU- 88	4.37	0	Hydrophobic	false
C5'	CD1	LEU- 88	4.45	0	Hydrophobic	false
C5A	CD1	LEU- 88	3.97	0	Hydrophobic	false
C6	CD1	LEU- 108	3.88	0	Hydrophobic	false
C5'	CD1	LEU- 108	3.76	0	Hydrophobic	false
C6	CD2	TYR- 145	3.79	0	Hydrophobic	false
O2	N	GLY- 146	3.17	134.07	H-Bond (Protein Donor)	false
O3	N	GLY- 146	3.3	133.92	H-Bond (Protein Donor)	false
O2	OE2	GLU- 161	2.63	169.58	H-Bond (Ligand Donor)	false
O3	OE1	GLU- 161	2.82	162.13	H-Bond (Ligand Donor)	false
O3P	NZ	LYS- 162	2.85	160.96	H-Bond (Protein Donor)	false
O3P	NZ	LYS- 162	2.85	0	Ionic (Protein Cationic)	false
O4	OH	TYR- 176	2.88	158.49	H-Bond (Ligand Donor)	false
O4P	NH2	ARG- 194	2.69	150.96	H-Bond (Protein Donor)	false
O3P	NH2	ARG- 194	3.34	131.88	H-Bond (Protein Donor)	false
O3P	NH1	ARG- 194	2.76	165.78	H-Bond (Protein Donor)	false
O4P	CZ	ARG- 194	3.68	0	Ionic (Protein Cationic)	false
O3P	CZ	ARG- 194	3.49	0	Ionic (Protein Cationic)	false
C3	CG2	ILE- 199	3.83	0	Hydrophobic	false
C6	CZ2	TRP- 223	3.97	0	Hydrophobic	false
O4P	O	HOH- 614	2.86	179.96	H-Bond (Protein Donor)	false
O3'	O	HOH- 635	2.75	159.56	H-Bond (Ligand Donor)	false