scPDB - 2ixk entry

Protein Data Bank Entry:

PDB ID : 2ixk

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2006-07-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	dTDP-4-dehydrorhamnose 3,5-epimerase
ID:	RMLC_PSEAE
AC:	Q9HU21
Organism:	Pseudomonas aeruginosa
Reign:	Bacteria
TaxID:	208964
EC Number:	5.1.3.13

Chains:

Chain Name:	Percentage of Residues within binding site
A	78 %
B	22 %

Ligand binding site composition:

B-Factor:	13.077
Number of residues:	42
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	6
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.397	580.500

% Hydrophobic	% Polar
43.60	56.40
According to VolSite

Ligand :

HET Code:	TDO
Formula:	C16H22N2O15P2
Molecular weight:	544.298 g/mol
DrugBank ID:	-
Buried Surface Area:	65.74 %
Polar Surface area:	273.19 Å2

Number of
H-Bond Acceptors:	15
H-Bond Donors:	4
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
17.6044	10.854	15.5967

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
C4'	CB	PHE- 22	3.96	0	Hydrophobic	false
C3'	CG	PHE- 22	4.41	0	Hydrophobic	false
C1'	CD1	PHE- 22	3.86	0	Hydrophobic	false
O4P	NH1	ARG- 26	2.91	164.51	H-Bond (Protein Donor)	false
O1P	NH2	ARG- 26	2.86	146.71	H-Bond (Protein Donor)	false
O4P	CZ	ARG- 26	3.75	0	Ionic (Protein Cationic)	false
O1P	CZ	ARG- 26	3.81	0	Ionic (Protein Cationic)	false
C1'	CD2	PHE- 29	4.08	0	Hydrophobic	false
C5A	CZ	PHE- 29	3.65	0	Hydrophobic	false
C5'	CB	PHE- 29	4.17	0	Hydrophobic	false
N31	OE2	GLU- 31	2.77	177.44	H-Bond (Ligand Donor)	false
O41	NE2	GLN- 50	2.8	138.93	H-Bond (Protein Donor)	false
O3P	CZ	ARG- 62	3.68	0	Ionic (Protein Cationic)	false
O3P	NH1	ARG- 62	2.77	151.59	H-Bond (Protein Donor)	false
C6	CB	ARG- 62	4.06	0	Hydrophobic	false
O4	NZ	LYS- 74	2.8	162.9	H-Bond (Protein Donor)	false
C5	CE2	PHE- 123	4.49	0	Hydrophobic	false
C6	CD2	PHE- 123	4.03	0	Hydrophobic	false
C3	CE1	TYR- 134	3.44	0	Hydrophobic	false
C5	CZ	TYR- 134	4.43	0	Hydrophobic	false
C2	CZ	TYR- 134	3.9	0	Hydrophobic	false
C5A	CE2	TRP- 140	4.46	0	Hydrophobic	false
C2'	CZ2	TRP- 140	3.57	0	Hydrophobic	false
O1P	NZ	LYS- 170	3.9	0	Ionic (Protein Cationic)	false
O2P	NZ	LYS- 170	2.71	0	Ionic (Protein Cationic)	false
O2P	NZ	LYS- 170	2.71	154.17	H-Bond (Protein Donor)	false
O4P	O	HOH- 2246	2.9	172.81	H-Bond (Protein Donor)	false
O41	O	HOH- 2279	2.82	179.98	H-Bond (Protein Donor)	false
O2P	O	HOH- 2280	2.84	179.99	H-Bond (Protein Donor)	false