scPDB - 2o1x entry

Protein Data Bank Entry:

PDB ID : 2o1x

Resolution :2.900 Å

Experimental Method : X-ray

Deposition Date : 2006-11-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	6.940	6.940	6.940	0.000	6.940	1

List of CHEMBLId :

CHEMBL2104121

Binding Site :

Uniprot Annotation

Name:	1-deoxy-D-xylulose-5-phosphate synthase
ID:	DXS_DEIRA
AC:	Q9RUB5
Organism:	Deinococcus radiodurans
Reign:	Bacteria
TaxID:	243230
EC Number:	2.2.1.7

Chains:

Chain Name:	Percentage of Residues within binding site
C	2 %
D	98 %

Ligand binding site composition:

B-Factor:	59.194
Number of residues:	41
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
1.041	472.500

% Hydrophobic	% Polar
61.43	38.57
According to VolSite

Ligand :

HET Code:	TDP
Formula:	C12H16N4O7P2S
Molecular weight:	422.291 g/mol
DrugBank ID:	DB01987
Buried Surface Area:	73.09 %
Polar Surface area:	225.32 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	1
Rings:	2
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
16.9927	-67.6072	38.37

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
S1	CG1	VAL- 80	3.97	0	Hydrophobic	false
C5B	CG2	VAL- 80	4.29	0	Hydrophobic	false
O23	NE2	HIS- 82	3.05	123.92	H-Bond (Protein Donor)	false
N4'	O	GLY- 123	2.79	162.97	H-Bond (Ligand Donor)	false
C2A	CB	HIS- 124	4.22	0	Hydrophobic	false
C2A	CB	ALA- 125	4.34	0	Hydrophobic	false
N3'	N	ALA- 125	3.14	172.65	H-Bond (Protein Donor)	false
O12	N	GLY- 155	2.69	141.29	H-Bond (Protein Donor)	false
S1	CD1	ILE- 187	3.72	0	Hydrophobic	false
C4A	CD1	ILE- 187	4.29	0	Hydrophobic	false
C5A	CD1	ILE- 187	4.18	0	Hydrophobic	false
O21	NZ	LYS- 289	3.8	0	Ionic (Protein Cationic)	false
C4A	CB	ALA- 348	4.29	0	Hydrophobic	false
C4A	CE	MET- 349	3.89	0	Hydrophobic	false
C2A	CG2	ILE- 371	3.9	0	Hydrophobic	false
C4A	CD1	ILE- 371	3.34	0	Hydrophobic	false
C5B	CD1	ILE- 371	3.66	0	Hydrophobic	false
N1'	OE2	GLU- 373	3.03	138.34	H-Bond (Ligand Donor)	false
C2A	CD1	PHE- 398	4.35	0	Hydrophobic	false
DuAr	DuAr	PHE- 398	3.6	0	Aromatic Face/Face	false
O12	MG	MG- 2004	2.35	0	Metal Acceptor	false