scPDB - 3r0i entry

Protein Data Bank Entry:

PDB ID : 3r0i

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2011-03-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	1-deoxy-D-xylulose 5-phosphate reductoisomerase
ID:	DXR_ECOLI
AC:	P45568
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	1.1.1.267

Chains:

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

Ligand binding site composition:

B-Factor:	17.173
Number of residues:	28
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	MN

Cavity properties

Ligandability	Volume (Å3)
0.427	428.625

% Hydrophobic	% Polar
38.58	61.42
According to VolSite

Ligand :

HET Code:	C0K
Formula:	C11H12F2NO5P
Molecular weight:	307.187 g/mol
DrugBank ID:	-
Buried Surface Area:	46.95 %
Polar Surface area:	113.54 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	1
Rings:	1
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
8.673	-4.1604	36.7558

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
O9	OG	SER- 186	2.64	157.11	H-Bond (Protein Donor)	false
O11	N	SER- 186	3	151.81	H-Bond (Protein Donor)	false
C2	CB	SER- 186	3.71	0	Hydrophobic	false
O9	OG	SER- 222	3.06	147.05	H-Bond (Protein Donor)	false
C12	CB	SER- 222	4.31	0	Hydrophobic	false
O10	ND2	ASN- 227	2.5	142.18	H-Bond (Protein Donor)	false
O15	ND2	ASN- 227	3.12	148.17	H-Bond (Protein Donor)	false
O10	NZ	LYS- 228	3.26	128.36	H-Bond (Protein Donor)	false
O11	NZ	LYS- 228	2.95	138.49	H-Bond (Protein Donor)	false
O10	NZ	LYS- 228	3.26	0	Ionic (Protein Cationic)	false
O11	NZ	LYS- 228	2.95	0	Ionic (Protein Cationic)	false
F19	CB	SER- 254	3.64	0	Hydrophobic	false
F19	CB	PRO- 274	4.48	0	Hydrophobic	false
O9	O	HOH- 476	2.51	168.82	H-Bond (Protein Donor)	false
O15	MN	MN- 990	2.12	0	Metal Acceptor	false
O18	MN	MN- 990	2.07	0	Metal Acceptor	false