scPDB - 4to4 entry

Protein Data Bank Entry:

PDB ID : 4to4

Resolution :2.100 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
A	100 %

Ligand binding site composition:

B-Factor:	36.438
Number of residues:	35
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.579	1080.000

% Hydrophobic	% Polar
32.19	67.81
According to VolSite

Ligand :

HET Code:	DCP
Formula:	C9H12N3O13P3
Molecular weight:	463.125 g/mol
DrugBank ID:	DB03258
Buried Surface Area:	64.85 %
Polar Surface area:	288.71 Å2

Number of
H-Bond Acceptors:	15
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
7.20939	4.21943	32.044

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
O3'	NE2	GLN- 149	2.96	163.39	H-Bond (Protein Donor)	false
C2'	CD2	LEU- 150	3.55	0	Hydrophobic	false
O4'	NH2	ARG- 164	3.04	148.09	H-Bond (Protein Donor)	false
O1A	NH1	ARG- 164	3.12	125.39	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 164	3.76	0	Ionic (Protein Cationic)	false
O2B	NH2	ARG- 206	2.88	141.41	H-Bond (Protein Donor)	false
O1A	NE2	HIS- 210	2.9	130.99	H-Bond (Protein Donor)	false
O5'	NE2	HIS- 215	2.9	136.64	H-Bond (Protein Donor)	false
O1A	NE2	HIS- 215	2.98	142.63	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 312	2.91	162.47	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 312	2.91	0	Ionic (Protein Cationic)	false
C3'	CD1	TYR- 315	3.64	0	Hydrophobic	false
C4'	CD2	TYR- 315	4.08	0	Hydrophobic	false
C5'	CE2	TYR- 315	3.44	0	Hydrophobic	false
O1G	OH	TYR- 315	2.66	150.57	H-Bond (Protein Donor)	false
O3'	OD2	ASP- 319	2.56	148.69	H-Bond (Ligand Donor)	false
O1G	NE	ARG- 366	2.92	172.35	H-Bond (Protein Donor)	false
O1G	NH2	ARG- 366	3.48	135.14	H-Bond (Protein Donor)	false
O3G	NH2	ARG- 366	3.09	142.12	H-Bond (Protein Donor)	false
O1G	CZ	ARG- 366	3.66	0	Ionic (Protein Cationic)	false
O3G	CZ	ARG- 366	3.99	0	Ionic (Protein Cationic)	false
C1'	CD1	TYR- 374	4.46	0	Hydrophobic	false
C2'	CZ	TYR- 374	3.48	0	Hydrophobic	false
O2B	MG	MG- 702	2.47	0	Metal Acceptor	false
O2G	MG	MG- 702	2.19	0	Metal Acceptor	false
N4	O	HOH- 855	3.16	173.14	H-Bond (Ligand Donor)	false