scPDB - 4tnr entry

Protein Data Bank Entry:

PDB ID : 4tnr

Resolution :2.750 Å

Experimental Method : X-ray

Deposition Date : 2014-06-04

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	27 %
B	27 %
C	47 %

Ligand binding site composition:

B-Factor:	76.648
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)
0.759	1657.125

% Hydrophobic	% Polar
38.29	61.71
According to VolSite

Ligand :

HET Code:	DTP
Formula:	C10H12N5O12P3
Molecular weight:	487.150 g/mol
DrugBank ID:	DB03222
Buried Surface Area:	73.16 %
Polar Surface area:	299.64 Å2

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

Mass center Coordinates

X	Y	Z
-34.8162	7.9174	56.5682

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
N3	ND2	ASN- 119	3.16	140.18	H-Bond (Protein Donor)	false
C1'	CB	ASN- 119	3.46	0	Hydrophobic	false
C3'	CG1	VAL- 156	3.79	0	Hydrophobic	false
C2'	CZ	PHE- 157	3.32	0	Hydrophobic	false
C1'	CE2	PHE- 157	3.51	0	Hydrophobic	false
O1A	CZ	ARG- 333	3.92	0	Ionic (Protein Cationic)	false
O1A	NH2	ARG- 333	3.08	153.24	H-Bond (Protein Donor)	false
O4'	NH1	ARG- 333	3.18	128.79	H-Bond (Protein Donor)	false
DuAr	CZ	ARG- 333	3.67	25.27	Pi/Cation	false
O1G	NH2	ARG- 352	3.36	145.07	H-Bond (Protein Donor)	false
O1G	NH1	ARG- 352	3.19	154.54	H-Bond (Protein Donor)	false
O3G	NH2	ARG- 352	2.65	139.12	H-Bond (Protein Donor)	false
O1G	CZ	ARG- 352	3.74	0	Ionic (Protein Cationic)	false
O3G	CZ	ARG- 352	3.65	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 354	3.72	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 354	2.72	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 354	2.82	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 354	2.72	125.7	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 354	2.82	152.41	H-Bond (Protein Donor)	false
N6	OD1	ASN- 358	3.13	147.87	H-Bond (Ligand Donor)	false
O2A	NE2	HIS- 376	2.74	167.01	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 377	3.88	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 377	3.07	0	Ionic (Protein Cationic)	false
O1B	NZ	LYS- 377	3.74	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 377	3.95	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 377	3.07	159.5	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 523	3.54	0	Ionic (Protein Cationic)	false
O2G	NZ	LYS- 523	3.35	0	Ionic (Protein Cationic)	false
O2G	NZ	LYS- 523	3.35	175.32	H-Bond (Protein Donor)	false
O2G	MG	MG- 702	2.26	0	Metal Acceptor	false
O1B	MG	MG- 702	2.49	0	Metal Acceptor	false