scPDB - 4rxs entry

Protein Data Bank Entry:

PDB ID : 4rxs

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2014-12-11

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
A	100 %

Ligand binding site composition:

B-Factor:	41.813
Number of residues:	29
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.797	1677.375

% Hydrophobic	% Polar
32.80	67.20
According to VolSite

Ligand :

HET Code:	TTP
Formula:	C10H13N2O14P3
Molecular weight:	478.137 g/mol
DrugBank ID:	DB02452
Buried Surface Area:	60.61 %
Polar Surface area:	279.44 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	2
Rings:	2
Aromatic rings:	0
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
38.6937	31.7598	24.8334

Binding mode :

What is Poseview ?

2D View
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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	2.92	160.74	H-Bond (Protein Donor)	false
C2'	CD2	LEU- 150	3.62	0	Hydrophobic	false
O1G	NH1	ARG- 164	3.42	131.6	H-Bond (Protein Donor)	false
O3G	NH1	ARG- 164	2.88	130.66	H-Bond (Protein Donor)	false
O4'	NH2	ARG- 164	3.15	156.29	H-Bond (Protein Donor)	false
O3G	CZ	ARG- 164	3.54	0	Ionic (Protein Cationic)	false
O1G	NE2	HIS- 167	3.39	148.8	H-Bond (Protein Donor)	false
O3G	NE2	HIS- 210	3.32	151.73	H-Bond (Protein Donor)	false
O3G	NE2	HIS- 215	2.98	154.69	H-Bond (Protein Donor)	false
O2G	NE2	HIS- 233	3.07	137.79	H-Bond (Protein Donor)	false
O1A	OH	TYR- 315	3.49	132.83	H-Bond (Protein Donor)	false
C5'	CE2	TYR- 315	3.32	0	Hydrophobic	false
C4'	CD2	TYR- 315	3.84	0	Hydrophobic	false
C3'	CD1	TYR- 315	3.53	0	Hydrophobic	false
O3'	OD2	ASP- 319	2.67	152.74	H-Bond (Ligand Donor)	false
C2'	CZ	TYR- 374	3.4	0	Hydrophobic	false
O4	NE2	GLN- 375	3.37	123.39	H-Bond (Protein Donor)	false