scPDB - 2bmu entry

Protein Data Bank Entry:

PDB ID : 2bmu

Resolution :2.550 Å

Experimental Method : X-ray

Deposition Date : 2005-03-16

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_PYRFU
AC:	Q8U122
Organism:	Pyrococcus furiosus
Reign:	Archaea
TaxID:	186497
EC Number:	2.7.4.22

Chains:

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

Ligand binding site composition:

B-Factor:	37.558
Number of residues:	43
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	3
Water Molecules:	1
Cofactors:	ANP
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
0.175	246.375

% Hydrophobic	% Polar
38.36	61.64
According to VolSite

Ligand :

HET Code:	U5P
Formula:	C9H11N2O9P
Molecular weight:	322.165 g/mol
DrugBank ID:	-
Buried Surface Area:	85.04 %
Polar Surface area:	181.33 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	3
Rings:	2
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
84.2003	115.681	50.7314

Binding mode :

What is Poseview ?

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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
O2P	N	GLY- 44	2.67	165.64	H-Bond (Protein Donor)	false
C5'	CB	ALA- 48	4.19	0	Hydrophobic	false
C4'	CD1	ILE- 52	4.34	0	Hydrophobic	false
C1'	CB	ASP- 66	4.39	0	Hydrophobic	false
C1'	CG1	ILE- 70	4.39	0	Hydrophobic	false
C5'	CG2	THR- 73	4.22	0	Hydrophobic	false
O4	N	THR- 114	2.7	172.08	H-Bond (Protein Donor)	false
O4	OG1	THR- 114	3.21	163.57	H-Bond (Protein Donor)	false
N3	O	HIS- 115	2.73	163.98	H-Bond (Ligand Donor)	false
O3P	OG1	THR- 119	2.86	146.04	H-Bond (Protein Donor)	false
O1P	N	THR- 120	2.84	163.53	H-Bond (Protein Donor)	false
O3'	N	GLY- 179	3.42	148.22	H-Bond (Protein Donor)	false
O2'	O	HOH- 2006	3.37	124.59	H-Bond (Ligand Donor)	false