scPDB - 1onp entry

Protein Data Bank Entry:

PDB ID : 1onp

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2003-02-28

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
B	100 %

Ligand binding site composition:

B-Factor:	68.284
Number of residues:	23
Including
Standard Amino Acids:	22
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MN

Cavity properties

Ligandability	Volume (Å3)
0.801	921.375

% Hydrophobic	% Polar
41.76	58.24
According to VolSite

Ligand :

HET Code:	FOM
Formula:	C4H8NO5P
Molecular weight:	181.084 g/mol
DrugBank ID:	DB02948
Buried Surface Area:	63.06 %
Polar Surface area:	113.54 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	1
Rings:	0
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
29.2156	6.43827	12.5011

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
OP3	OG	SER- 186	2.52	158.39	H-Bond (Protein Donor)	false
C4	CB	SER- 222	4.25	0	Hydrophobic	false
OP3	OG	SER- 222	3	161	H-Bond (Protein Donor)	false
OP1	ND2	ASN- 227	2.6	154.44	H-Bond (Protein Donor)	false
OP1	NZ	LYS- 228	3.46	142.37	H-Bond (Protein Donor)	false
OP2	NZ	LYS- 228	2.93	139.32	H-Bond (Protein Donor)	false
OP1	NZ	LYS- 228	3.46	0	Ionic (Protein Cationic)	false
OP2	NZ	LYS- 228	2.93	0	Ionic (Protein Cationic)	false
O2	MN	MN- 1002	2.13	0	Metal Acceptor	false
O1	MN	MN- 1002	2.3	0	Metal Acceptor	false