scPDB - 4to5 entry

Protein Data Bank Entry:

PDB ID : 4to5

Resolution :2.800 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	33 %
B	23 %
C	43 %

Ligand binding site composition:

B-Factor:	85.655
Number of residues:	30
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:	GTP
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.760	1542.375

% Hydrophobic	% Polar
37.20	62.80
According to VolSite

Ligand :

HET Code:	TTP
Formula:	C10H13N2O14P3
Molecular weight:	478.137 g/mol
DrugBank ID:	DB02452
Buried Surface Area:	73.07 %
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
-14.1856	27.2737	-6.09369

Binding mode :

What is Poseview ?

2D View
3D View

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
C4'	CB	ASN- 119	4.38	0	Hydrophobic	false
C1'	CB	ASN- 119	3.47	0	Hydrophobic	false
O3'	N	ASN- 119	3.38	175.67	H-Bond (Protein Donor)	false
O2	ND2	ASN- 119	2.93	121.94	H-Bond (Protein Donor)	false
O3'	O	VAL- 156	2.76	146.68	H-Bond (Ligand Donor)	false
C3'	CG1	VAL- 156	4.01	0	Hydrophobic	false
C2'	CE1	PHE- 157	3.27	0	Hydrophobic	false
O2A	CZ	ARG- 333	3.62	0	Ionic (Protein Cationic)	false
O2A	NH2	ARG- 333	2.78	152.35	H-Bond (Protein Donor)	false
O1G	NH1	ARG- 352	3.07	159.01	H-Bond (Protein Donor)	false
O3G	NH2	ARG- 352	2.53	167.4	H-Bond (Protein Donor)	false
O1G	CZ	ARG- 352	3.82	0	Ionic (Protein Cationic)	false
O3G	CZ	ARG- 352	3.5	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 354	2.57	147.24	H-Bond (Protein Donor)	false
O3A	NZ	LYS- 354	3.46	142.96	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 354	2.71	153.22	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 354	2.57	0	Ionic (Protein Cationic)	false
O1G	NZ	LYS- 354	2.71	0	Ionic (Protein Cationic)	false
O4	ND2	ASN- 358	3.43	157.99	H-Bond (Protein Donor)	false
O4	NH2	ARG- 372	2.73	137.89	H-Bond (Protein Donor)	false
O1A	NE2	HIS- 376	2.75	162.23	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 377	3.63	0	Ionic (Protein Cationic)	false
O3B	NZ	LYS- 377	2.96	158.97	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 523	2.69	135.95	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 523	2.69	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 523	3.78	0	Ionic (Protein Cationic)	false
O3A	O3'	GTP- 701	3.17	136.96	H-Bond (Protein Donor)	false
O2B	O3'	GTP- 701	3.04	147.13	H-Bond (Protein Donor)	false
C3'	C1'	GTP- 701	4.45	0	Hydrophobic	false
O2B	MG	MG- 704	1.91	0	Metal Acceptor	false
O2G	MG	MG- 704	1.92	0	Metal Acceptor	false