scPDB - 3fd6 entry

Protein Data Bank Entry:

PDB ID : 3fd6

Resolution :1.950 Å

Experimental Method : X-ray

Deposition Date : 2008-11-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Selenide, water dikinase 1
ID:	SPS1_HUMAN
AC:	P49903
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.9.3

Chains:

Chain Name:	Percentage of Residues within binding site
A	69 %
B	31 %

Ligand binding site composition:

B-Factor:	19.018
Number of residues:	39
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	4
Water Molecules:	2
Cofactors:
Metals:	MG MG MG NA

Cavity properties

Ligandability	Volume (Å3)
0.561	546.750

% Hydrophobic	% Polar
42.59	57.41
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	73.08 %
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
65.1126	31.9344	83.2252

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
O1A	NZ	LYS- 32	3.68	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 32	2.96	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 32	2.96	164.5	H-Bond (Protein Donor)	false
C5'	CD2	LEU- 38	3.74	0	Hydrophobic	false
C1'	CD1	LEU- 42	3.95	0	Hydrophobic	false
C4'	CG2	ILE- 66	4.35	0	Hydrophobic	false
C1'	CG2	ILE- 66	3.63	0	Hydrophobic	false
O3'	N	GLY- 67	3.15	153.36	H-Bond (Protein Donor)	false
O3'	O	MET- 68	2.54	175.99	H-Bond (Ligand Donor)	false
O2'	N	GLY- 162	3.01	160.22	H-Bond (Protein Donor)	false
N7	OG1	THR- 164	2.8	149.81	H-Bond (Protein Donor)	false
N6	OG1	THR- 164	3.26	156.69	H-Bond (Ligand Donor)	false
O3B	MG	MG- 395	2.54	0	Metal Acceptor	false
O1B	MG	MG- 396	2.62	0	Metal Acceptor	false
O2B	MG	MG- 396	2.67	0	Metal Acceptor	false
O1B	MG	MG- 397	2.71	0	Metal Acceptor	false
O1A	MG	MG- 397	2.13	0	Metal Acceptor	false
O2'	O	HOH- 429	3.44	164.03	H-Bond (Ligand Donor)	false