scPDB - 1s4e entry

Protein Data Bank Entry:

PDB ID : 1s4e

Resolution :2.900 Å

Experimental Method : X-ray

Deposition Date : 2004-01-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Galactokinase
ID:	GAL1_PYRFU
AC:	Q9HHB6
Organism:	Pyrococcus furiosus
Reign:	Archaea
TaxID:	186497
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	33.923
Number of residues:	29
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.107	604.125

% Hydrophobic	% Polar
41.90	58.10
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	60.16 %
Polar Surface area:	260.7 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
122.49	152.009	65.2634

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
N1	OG	SER- 49	2.87	160.67	H-Bond (Protein Donor)	false
C2'	CE1	PHE- 52	4.1	0	Hydrophobic	false
C2'	CB	TRP- 69	3.8	0	Hydrophobic	false
C5'	CZ	TYR- 72	4.42	0	Hydrophobic	false
C4'	CE1	TYR- 72	3.65	0	Hydrophobic	false
C1'	CE1	TYR- 72	3.54	0	Hydrophobic	false
C3'	CD2	LEU- 100	3.97	0	Hydrophobic	false
O2B	N	GLY- 101	2.86	137.27	H-Bond (Protein Donor)	false
O2B	N	ALA- 102	3.39	142.88	H-Bond (Protein Donor)	false
O2B	N	SER- 106	3.38	142.21	H-Bond (Protein Donor)	false
O2B	OG	SER- 106	2.63	148.55	H-Bond (Protein Donor)	false
C5'	CB	SER- 106	4.35	0	Hydrophobic	false
O3B	N	SER- 107	2.78	174.07	H-Bond (Protein Donor)	false
C5'	CB	SER- 107	4.11	0	Hydrophobic	false
C1'	CD1	PHE- 110	4.01	0	Hydrophobic	false
O1B	MG	MG- 8600	2.4	0	Metal Acceptor	false
O3B	MG	MG- 8600	2.72	0	Metal Acceptor	false
O2A	MG	MG- 8600	2.14	0	Metal Acceptor	false