scPDB - 2iw1 entry

Protein Data Bank Entry:

PDB ID : 2iw1

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 2006-06-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Lipopolysaccharide core biosynthesis protein RfaG
ID:	RFAG_ECOLI
AC:	P25740
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	2.4

Chains:

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

Ligand binding site composition:

B-Factor:	8.075
Number of residues:	53
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	0
Water Molecules:	6
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.221	874.125

% Hydrophobic	% Polar
32.82	67.18
According to VolSite

Ligand :

HET Code:	U2F
Formula:	C15H21FN2O16P2
Molecular weight:	566.277 g/mol
DrugBank ID:	DB03488
Buried Surface Area:	77.53 %
Polar Surface area:	296.59 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	6
Rings:	3
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
-5.63092	10.8896	-19.0942

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
O1B	N	GLY- 15	2.75	168.49	H-Bond (Protein Donor)	false
C1'	CD	ARG- 18	3.69	0	Hydrophobic	false
C4'	CD	ARG- 18	3.98	0	Hydrophobic	false
O6	OD2	ASP- 19	2.74	159.43	H-Bond (Ligand Donor)	false
C6	CE2	PHE- 97	4.24	0	Hydrophobic	false
C6	CB	ALA- 99	3.87	0	Hydrophobic	false
C4	CD1	LEU- 143	4.45	0	Hydrophobic	false
C6	CD1	LEU- 143	3.82	0	Hydrophobic	false
O2'	NH2	ARG- 173	3.08	142.02	H-Bond (Protein Donor)	false
C2'	CG1	VAL- 202	4.18	0	Hydrophobic	false
O2B	CZ	ARG- 208	3.83	0	Ionic (Protein Cationic)	false
O2B	NH2	ARG- 208	2.78	157.67	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 209	2.82	152.13	H-Bond (Protein Donor)	false
O3A	NZ	LYS- 209	2.93	127.47	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 209	2.82	0	Ionic (Protein Cationic)	false
N3	O	ARG- 261	2.83	173.19	H-Bond (Ligand Donor)	false
O7'	N	ARG- 261	2.98	165.35	H-Bond (Protein Donor)	false
O3	OE2	GLU- 281	2.67	155.4	H-Bond (Ligand Donor)	false
O3	N	ALA- 283	2.96	166.11	H-Bond (Protein Donor)	false
C4	CB	ALA- 283	4.16	0	Hydrophobic	false
O4	N	GLY- 284	2.93	164.89	H-Bond (Protein Donor)	false
O1A	N	ILE- 285	2.79	158.88	H-Bond (Protein Donor)	false
C3'	CG2	ILE- 285	4	0	Hydrophobic	false
C6	CD1	ILE- 285	4.13	0	Hydrophobic	false
O2A	N	VAL- 286	3.14	160.43	H-Bond (Protein Donor)	false
C5'	CG1	VAL- 286	4.46	0	Hydrophobic	false
C2'	CG1	VAL- 286	3.74	0	Hydrophobic	false
O3'	OE2	GLU- 289	2.63	174.35	H-Bond (Ligand Donor)	false
O2'	OE2	GLU- 289	3.09	131.14	H-Bond (Ligand Donor)	false
O2'	OE1	GLU- 289	2.65	162.74	H-Bond (Ligand Donor)	false
O2A	O	HOH- 2583	2.73	138.17	H-Bond (Protein Donor)	false
O1B	O	HOH- 2584	2.78	175.61	H-Bond (Protein Donor)	false