scPDB - 1mp5 entry

Protein Data Bank Entry:

PDB ID : 1mp5

Resolution :2.750 Å

Experimental Method : X-ray

Deposition Date : 2002-09-11

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:	RMLA_SALTY
AC:	P26393
Organism:	Salmonella typhimurium
Reign:	Bacteria
TaxID:	99287
EC Number:	2.7.7.24

Chains:

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

Ligand binding site composition:

B-Factor:	31.049
Number of residues:	39
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.434	1076.625

% Hydrophobic	% Polar
34.17	65.83
According to VolSite

Ligand :

HET Code:	UPG
Formula:	C15H22N2O17P2
Molecular weight:	564.286 g/mol
DrugBank ID:	DB01861
Buried Surface Area:	59.68 %
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
-25.4669	70.9079	24.2897

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
O1A	NH2	ARG- 16	3.26	164.49	H-Bond (Protein Donor)	false
O2A	NH2	ARG- 16	3.46	120.87	H-Bond (Protein Donor)	false
O2A	NH1	ARG- 16	3.33	122.86	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 16	3.9	0	Ionic (Protein Cationic)	false
O2A	CZ	ARG- 16	3.74	0	Ionic (Protein Cationic)	false
C5C	CD2	LEU- 89	3.62	0	Hydrophobic	false
C1'	CD1	LEU- 89	3.69	0	Hydrophobic	false
C6'	CD1	LEU- 109	4.31	0	Hydrophobic	false
C4C	CD2	LEU- 109	4.22	0	Hydrophobic	false
O3C	OD2	ASP- 111	3.15	148.61	H-Bond (Ligand Donor)	false
C4'	CB	TYR- 146	4.25	0	Hydrophobic	false
C6'	CD2	TYR- 146	3.65	0	Hydrophobic	false
O4'	N	GLY- 147	3.11	171.95	H-Bond (Protein Donor)	false
O2'	OE2	GLU- 162	2.77	167.06	H-Bond (Ligand Donor)	false
O2'	OE1	GLU- 162	3.15	125.02	H-Bond (Ligand Donor)	false
O3'	OE1	GLU- 162	2.97	159.8	H-Bond (Ligand Donor)	false
O1B	NZ	LYS- 163	2.76	149.32	H-Bond (Protein Donor)	false
O3B	NZ	LYS- 163	3.42	139.57	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 163	2.76	0	Ionic (Protein Cationic)	false
O4'	O	VAL- 173	2.76	164.76	H-Bond (Ligand Donor)	false
O1B	NH1	ARG- 195	3.19	170.02	H-Bond (Protein Donor)	false
O2B	NH1	ARG- 195	3.08	122.27	H-Bond (Protein Donor)	false
O2B	NH2	ARG- 195	2.97	124.64	H-Bond (Protein Donor)	false
O2B	CZ	ARG- 195	3.36	0	Ionic (Protein Cationic)	false
C2'	CG2	ILE- 200	3.55	0	Hydrophobic	false
C6'	CZ2	TRP- 224	4.23	0	Hydrophobic	false