scPDB - 3pkp entry

Protein Data Bank Entry:

PDB ID : 3pkp

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2010-11-11

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
I	3 %
J	97 %

Ligand binding site composition:

B-Factor:	62.391
Number of residues:	33
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
0.868	1491.750

% Hydrophobic	% Polar
29.19	70.81
According to VolSite

Ligand :

HET Code:	DTP
Formula:	C10H12N5O12P3
Molecular weight:	487.150 g/mol
DrugBank ID:	DB03222
Buried Surface Area:	67.8 %
Polar Surface area:	299.64 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	2
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
83.8639	-20.549	11.2926

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
C1'	CB	LEU- 9	4.33	0	Hydrophobic	false
N3	N	GLY- 11	3.05	147.65	H-Bond (Protein Donor)	false
O1B	N	GLY- 14	2.73	157.33	H-Bond (Protein Donor)	false
O1G	OG1	THR- 15	3.43	142.34	H-Bond (Protein Donor)	false
O1G	N	ARG- 16	3.03	166.02	H-Bond (Protein Donor)	false
O1G	NE	ARG- 16	2.91	169.59	H-Bond (Protein Donor)	false
O3G	NE	ARG- 16	3.33	129.85	H-Bond (Protein Donor)	false
O3G	NH2	ARG- 16	3.23	130.95	H-Bond (Protein Donor)	false
O1G	CZ	ARG- 16	3.68	0	Ionic (Protein Cationic)	false
O3G	CZ	ARG- 16	3.65	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 26	3.32	126.03	H-Bond (Protein Donor)	false
O3A	NZ	LYS- 26	3.08	166.73	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 26	3.32	0	Ionic (Protein Cationic)	false
O3'	OE1	GLN- 27	2.95	157.84	H-Bond (Ligand Donor)	false
N6	OG	SER- 83	3.19	146.94	H-Bond (Ligand Donor)	false
N6	O	SER- 85	2.95	129.93	H-Bond (Ligand Donor)	false
N6	O	PRO- 86	2.97	165.82	H-Bond (Ligand Donor)	false
C5'	CD2	LEU- 89	4.45	0	Hydrophobic	false
C5'	CD1	LEU- 109	4.11	0	Hydrophobic	false
C4'	CB	LEU- 109	4.06	0	Hydrophobic	false
C3'	CB	ASP- 111	4.31	0	Hydrophobic	false
O3'	N	ASP- 111	3.06	125.14	H-Bond (Protein Donor)	false
O3G	NZ	LYS- 278	3.72	0	Ionic (Protein Cationic)	false
O2A	MG	MG- 501	2.31	0	Metal Acceptor	false
O2B	MG	MG- 502	2.62	0	Metal Acceptor	false
O1A	MG	MG- 502	2.45	0	Metal Acceptor	false