scPDB - 2pul entry

Protein Data Bank Entry:

PDB ID : 2pul

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2007-05-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Methylthioribose kinase
ID:	MTNK_BACSU
AC:	O31663
Organism:	Bacillus subtilis
Reign:	Bacteria
TaxID:	224308
EC Number:	2.7.1.100

Chains:

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

Ligand binding site composition:

B-Factor:	30.602
Number of residues:	32
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.891	563.625

% Hydrophobic	% Polar
53.89	46.11
According to VolSite

Ligand :

HET Code:	ACP
Formula:	C11H14N5O12P3
Molecular weight:	501.176 g/mol
DrugBank ID:	DB03909
Buried Surface Area:	54.09 %
Polar Surface area:	310.64 Å2

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

Mass center Coordinates

X	Y	Z
-67.8858	24.3047	7.47174

Binding mode :

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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'	CD1	ILE- 38	3.94	0	Hydrophobic	false
C5'	CB	ASP- 40	3.75	0	Hydrophobic	false
O1B	ND2	ASN- 44	3	165.71	H-Bond (Protein Donor)	false
C5'	CG2	VAL- 46	4.19	0	Hydrophobic	false
C1'	CG1	VAL- 46	4.1	0	Hydrophobic	false
O2B	NZ	LYS- 61	3.04	127.74	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 61	2.85	174.17	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 61	3.04	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 61	2.85	0	Ionic (Protein Cationic)	false
N6	O	GLU- 115	2.95	149.9	H-Bond (Ligand Donor)	false
N1	N	LEU- 117	2.79	158.87	H-Bond (Protein Donor)	false
C3'	CD1	ILE- 122	4.39	0	Hydrophobic	false
C2'	CZ	PHE- 240	3.76	0	Hydrophobic	false
O2G	MG	MG- 400	2.21	0	Metal Acceptor	false
O2B	MG	MG- 400	2.08	0	Metal Acceptor	false