scPDB - 3n2i entry

Protein Data Bank Entry:

PDB ID : 3n2i

Resolution :2.250 Å

Experimental Method : X-ray

Deposition Date : 2010-05-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Thymidylate kinase
ID:	KTHY_VIBCH
AC:	Q9KQI2
Organism:	Vibrio cholerae serotype O1
Reign:	Bacteria
TaxID:	243277
EC Number:	2.7.4.9

Chains:

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

Ligand binding site composition:

B-Factor:	57.754
Number of residues:	27
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.201	783.000

% Hydrophobic	% Polar
42.24	57.76
According to VolSite

Ligand :

HET Code:	THM
Formula:	C10H14N2O5
Molecular weight:	242.229 g/mol
DrugBank ID:	DB04485
Buried Surface Area:	77.41 %
Polar Surface area:	99.1 Å2

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

Mass center Coordinates

X	Y	Z
17.1865	-3.51935	20.8706

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
O3'	O	GLU- 40	3.38	120.8	H-Bond (Ligand Donor)	false
C5M	CB	GLU- 40	3.85	0	Hydrophobic	false
C4'	CG	LYS- 55	4.29	0	Hydrophobic	false
O4	NH2	ARG- 76	2.96	157.7	H-Bond (Protein Donor)	false
C5M	CB	ARG- 98	4.02	0	Hydrophobic	false
C2'	CD	ARG- 98	3.89	0	Hydrophobic	false
C5M	CB	SER- 102	3.77	0	Hydrophobic	false
C2'	CE1	TYR- 106	4.48	0	Hydrophobic	false
C1'	CD1	TYR- 106	4.46	0	Hydrophobic	false
O2	NE2	GLN- 107	2.96	162.54	H-Bond (Protein Donor)	false
N3	OE1	GLN- 107	2.72	175.74	H-Bond (Ligand Donor)	false
C5'	CD1	ILE- 157	4.21	0	Hydrophobic	false
C1'	CD1	ILE- 157	4.11	0	Hydrophobic	false