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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

4tnx

2.310 Å

X-ray

2014-06-05

Interactomes:
Molecular Function:
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
A26 %
B29 %
D45 %


Ligand binding site composition:

B-Factor:40.154
Number of residues:33
Including
Standard Amino Acids: 29
Non Standard Amino Acids: 2
Water Molecules: 2
Cofactors: GTP
Metals: MG

Cavity properties

LigandabilityVolume (Å3)
0.2872419.875

% Hydrophobic% Polar
38.9161.09
According to VolSite

Ligand :
4tnx_2 Structure
HET Code: DGT
Formula: C10H12N5O13P3
Molecular weight: 503.149 g/mol
DrugBank ID: DB02181
Buried Surface Area:75 %
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

XYZ
0.460419-11.6215-3.52887


Binding mode :
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Binding mode
BioSolveIT 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
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
O3'NASN- 1192.96166.67H-Bond
(Protein Donor)
C1'CBASN- 1193.60Hydrophobic
O3'OVAL- 1562.66154.86H-Bond
(Ligand Donor)
C2'CG1VAL- 1563.590Hydrophobic
C2'CZPHE- 1573.510Hydrophobic
C1'CE1PHE- 1573.460Hydrophobic
O1ANH2ARG- 3332.74160.79H-Bond
(Protein Donor)
O4'NH1ARG- 3333.22131.22H-Bond
(Protein Donor)
O1ACZARG- 3333.670Ionic
(Protein Cationic)
DuArCZARG- 3333.6318.05Pi/Cation
O2GNH2ARG- 3522.94145.68H-Bond
(Protein Donor)
O3GNH2ARG- 3523.12138.68H-Bond
(Protein Donor)
O3GNH1ARG- 3522.93147.5H-Bond
(Protein Donor)
O3GCZARG- 3523.440Ionic
(Protein Cationic)
O2ANZLYS- 3543.550Ionic
(Protein Cationic)
O6ND2ASN- 3583.03162.23H-Bond
(Protein Donor)
O6NEARG- 3723.23120.29H-Bond
(Protein Donor)
O2ANE2HIS- 3762.6163.99H-Bond
(Protein Donor)
O2GNZLYS- 3773.540Ionic
(Protein Cationic)
O1BNZLYS- 3772.570Ionic
(Protein Cationic)
O2ANZLYS- 3773.880Ionic
(Protein Cationic)
O3BNZLYS- 3772.92147.83H-Bond
(Protein Donor)
O1BNZLYS- 3772.57124.07H-Bond
(Protein Donor)
O1GNZLYS- 5233.05154.24H-Bond
(Protein Donor)
O1GNZLYS- 5233.050Ionic
(Protein Cationic)
O2GNZLYS- 5233.690Ionic
(Protein Cationic)
O2BMG MG- 7031.90Metal Acceptor
O2BO3'GTP- 7042.7148.42H-Bond
(Protein Donor)
O3AO3'GTP- 7043.4135.56H-Bond
(Protein Donor)
C5'C3'GTP- 7044.40Hydrophobic
C3'C1'GTP- 7044.180Hydrophobic