scPDB - 4ho6 entry

Protein Data Bank Entry:

PDB ID : 4ho6

Resolution :1.920 Å

Experimental Method : X-ray

Deposition Date : 2012-10-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glucose-1-phosphate thymidylyltransferase
ID:	Q9AGY4_ANETH
AC:	Q9AGY4
Organism:	Aneurinibacillus thermoaerophilus
Reign:	Bacteria
TaxID:	143495
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	26.654
Number of residues:	45
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.010	472.500

% Hydrophobic	% Polar
47.14	52.86
According to VolSite

Ligand :

HET Code:	UPG
Formula:	C15H22N2O17P2
Molecular weight:	564.286 g/mol
DrugBank ID:	DB01861
Buried Surface Area:	62.2 %
Polar Surface area:	316.82 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	7
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
-2.49083	-20.0823	-17.2384

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
O2	N	GLY- 8	2.94	134.16	H-Bond (Protein Donor)	false
O2C	O	GLY- 8	3.32	149.39	H-Bond (Ligand Donor)	false
N3	OE1	GLN- 80	2.77	165.09	H-Bond (Ligand Donor)	false
O4	NE2	GLN- 80	2.88	130.15	H-Bond (Protein Donor)	false
O4	N	GLY- 85	2.85	154.27	H-Bond (Protein Donor)	false
C5C	CD1	LEU- 86	4.2	0	Hydrophobic	false
C2'	CD2	LEU- 86	4.04	0	Hydrophobic	false
C6'	CD1	LEU- 106	4.25	0	Hydrophobic	false
C5C	CD1	LEU- 106	3.6	0	Hydrophobic	false
C6'	CD1	PHE- 143	4.16	0	Hydrophobic	false
O3'	N	GLY- 144	3.17	123	H-Bond (Protein Donor)	false
O4'	N	GLY- 144	3.01	145.14	H-Bond (Protein Donor)	false
O2'	OE2	GLU- 159	2.75	166.31	H-Bond (Ligand Donor)	false
O3'	OE1	GLU- 159	2.61	175.4	H-Bond (Ligand Donor)	false
O3'	OE2	GLU- 159	3.46	127.67	H-Bond (Ligand Donor)	false
O2B	NZ	LYS- 160	3.02	131.08	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 160	3.02	0	Ionic (Protein Cationic)	false
O4'	O	VAL- 170	2.68	175.04	H-Bond (Ligand Donor)	false
O1B	CZ	ARG- 192	3.57	0	Ionic (Protein Cationic)	false
O2B	CZ	ARG- 192	3.79	0	Ionic (Protein Cationic)	false
O1B	NH1	ARG- 192	3.12	146.68	H-Bond (Protein Donor)	false
O1B	NH2	ARG- 192	3.11	148.9	H-Bond (Protein Donor)	false
O2B	NH2	ARG- 192	2.96	133.31	H-Bond (Protein Donor)	false
C2'	CG2	ILE- 197	4.04	0	Hydrophobic	false
C6'	CZ2	TRP- 221	3.93	0	Hydrophobic	false
O2'	O	HOH- 402	3.07	151.94	H-Bond (Protein Donor)	false
O3C	O	HOH- 413	2.82	155.95	H-Bond (Ligand Donor)	false