scPDB - 4tny entry

Protein Data Bank Entry:

PDB ID : 4tny

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2014-06-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
ID:	SAMH1_HUMAN
AC:	Q9Y3Z3
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.1.5

Chains:

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

Ligand binding site composition:

B-Factor:	55.978
Number of residues:	35
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.799	1667.250

% Hydrophobic	% Polar
34.01	65.99
According to VolSite

Ligand :

HET Code:	DGT
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB02181
Buried Surface Area:	60.2 %
Polar Surface area:	315.33 Å2

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

Mass center Coordinates

X	Y	Z
38.6733	9.2771	-33.7618

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
O3'	NE2	GLN- 149	3.03	158.8	H-Bond (Protein Donor)	false
C2'	CD2	LEU- 150	3.61	0	Hydrophobic	false
O4'	NH2	ARG- 164	3.35	153.84	H-Bond (Protein Donor)	false
O2B	CZ	ARG- 206	3.53	0	Ionic (Protein Cationic)	false
O1A	NE2	HIS- 215	3.41	142.43	H-Bond (Protein Donor)	false
O5'	NE2	HIS- 215	3.16	136.33	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 312	3.58	0	Ionic (Protein Cationic)	false
O2G	NZ	LYS- 312	3.77	0	Ionic (Protein Cationic)	false
C5'	CE2	TYR- 315	3.39	0	Hydrophobic	false
C4'	CD2	TYR- 315	4.19	0	Hydrophobic	false
C3'	CD1	TYR- 315	3.79	0	Hydrophobic	false
O3'	OD2	ASP- 319	2.84	156.2	H-Bond (Ligand Donor)	false
O2G	NH2	ARG- 366	2.98	147.18	H-Bond (Protein Donor)	false
O2G	NE	ARG- 366	3.31	136.02	H-Bond (Protein Donor)	false
O2G	CZ	ARG- 366	3.56	0	Ionic (Protein Cationic)	false
C3'	CZ	TYR- 374	4.15	0	Hydrophobic	false
C2'	CE1	TYR- 374	3.59	0	Hydrophobic	false
O6	NE2	GLN- 375	2.77	132.04	H-Bond (Protein Donor)	false