scPDB - 2j4l entry

Protein Data Bank Entry:

PDB ID : 2j4l

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2006-09-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Uridylate kinase
ID:	PYRH_SULSO
AC:	Q97ZE2
Organism:	Sulfolobus solfataricus
Reign:	Archaea
TaxID:	273057
EC Number:	2.7.4.22

Chains:

Chain Name:	Percentage of Residues within binding site
D	4 %
F	96 %

Ligand binding site composition:

B-Factor:	62.587
Number of residues:	48
Including
Standard Amino Acids:	48
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.426	580.500

% Hydrophobic	% Polar
42.44	57.56
According to VolSite

Ligand :

HET Code:	UTP
Formula:	C9H11N2O15P3
Molecular weight:	480.109 g/mol
DrugBank ID:	DB04005
Buried Surface Area:	72.08 %
Polar Surface area:	299.67 Å2

Number of
H-Bond Acceptors:	15
H-Bond Donors:	3
Rings:	2
Aromatic rings:	0
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-36.8208	6.26579	-60.1099

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
O2B	NZ	LYS- 6	3.41	0	Ionic (Protein Cationic)	false
O1G	NZ	LYS- 6	3.17	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 6	3.99	0	Ionic (Protein Cationic)	false
O1G	NZ	LYS- 6	3.17	129.99	H-Bond (Protein Donor)	false
O1G	OG	SER- 8	2.51	145.09	H-Bond (Protein Donor)	false
O2G	OG	SER- 8	3.28	126.15	H-Bond (Protein Donor)	false
O2B	N	GLY- 9	3.05	121.97	H-Bond (Protein Donor)	false
O1G	N	GLY- 9	2.64	142.94	H-Bond (Protein Donor)	false
O2A	N	GLY- 43	3.1	153.47	H-Bond (Protein Donor)	false
O1B	N	GLY- 44	3.26	134.88	H-Bond (Protein Donor)	false
C5'	CB	ALA- 47	4.48	0	Hydrophobic	false
C4'	CD1	ILE- 51	4.4	0	Hydrophobic	false
O2'	OD1	ASP- 65	2.58	148.19	H-Bond (Ligand Donor)	false
C1'	CG1	ILE- 69	4.46	0	Hydrophobic	false
O4	N	PHE- 113	3.03	165.51	H-Bond (Protein Donor)	false
N3	O	GLN- 114	2.77	173.88	H-Bond (Ligand Donor)	false
O4	NE2	GLN- 117	3.27	141.27	H-Bond (Protein Donor)	false
O1A	N	THR- 119	3.25	152.17	H-Bond (Protein Donor)	false
O2A	OG1	THR- 119	2.62	156.8	H-Bond (Protein Donor)	false
C2'	CA	GLY- 179	4.08	0	Hydrophobic	false