scPDB - 2bri entry

Protein Data Bank Entry:

PDB ID : 2bri

Resolution :3.000 Å

Experimental Method : X-ray

Deposition Date : 2005-05-05

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:	59.594
Number of residues:	40
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.425	685.125

% Hydrophobic	% Polar
34.48	65.52
According to VolSite

Ligand :

HET Code:	ANP
Formula:	C10H13N6O12P3
Molecular weight:	502.164 g/mol
DrugBank ID:	-
Buried Surface Area:	62.99 %
Polar Surface area:	322.68 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
81.6521	129.676	49.4688

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
O1G	N	GLY- 9	3.26	168.95	H-Bond (Protein Donor)	false
O3G	N	GLY- 9	3.08	124.98	H-Bond (Protein Donor)	false
O3G	N	SER- 10	3.4	140.13	H-Bond (Protein Donor)	false
O2B	OG1	THR- 140	3.13	135.74	H-Bond (Protein Donor)	false
O2B	N	ASN- 141	3.2	125.19	H-Bond (Protein Donor)	false
N6	O	TYR- 146	2.7	157.14	H-Bond (Ligand Donor)	false
N1	N	TYR- 146	3.07	147.95	H-Bond (Protein Donor)	false
O2'	OD2	ASP- 149	2.57	147.06	H-Bond (Ligand Donor)	false
O1B	MG	MG- 1227	2.59	0	Metal Acceptor	false