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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:

4tnq

2.550 Å

X-ray

2014-06-04

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
A47 %
C33 %
D20 %


Ligand binding site composition:

B-Factor:42.643
Number of residues:31
Including
Standard Amino Acids: 28
Non Standard Amino Acids: 2
Water Molecules: 1
Cofactors: GTP
Metals: MG

Cavity properties

LigandabilityVolume (Å3)
0.4421981.125

% Hydrophobic% Polar
37.3162.69
According to VolSite

Ligand :
4tnq_5 Structure
HET Code: TTP
Formula: C10H13N2O14P3
Molecular weight: 478.137 g/mol
DrugBank ID: DB02452
Buried Surface Area:72.13 %
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

XYZ
101.734-23.5593129.279


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- 1193.11170.32H-Bond
(Protein Donor)
O2ND2ASN- 1192.82137.87H-Bond
(Protein Donor)
C1'CBASN- 1193.690Hydrophobic
O3'OVAL- 1562.74168.72H-Bond
(Ligand Donor)
C2'CG1VAL- 1563.890Hydrophobic
C2'CZPHE- 1573.270Hydrophobic
C1'CE1PHE- 1573.480Hydrophobic
O1ACZARG- 3333.450Ionic
(Protein Cationic)
O1ANH2ARG- 3332.77156.77H-Bond
(Protein Donor)
O1ANH1ARG- 3333.25132.57H-Bond
(Protein Donor)
O1GCZARG- 3523.810Ionic
(Protein Cationic)
O2GCZARG- 3523.520Ionic
(Protein Cationic)
O1GNH2ARG- 3522.76155.98H-Bond
(Protein Donor)
O2GNH1ARG- 3522.91152.85H-Bond
(Protein Donor)
O2GNH2ARG- 3523.25135.94H-Bond
(Protein Donor)
O1ANZLYS- 3542.76152.68H-Bond
(Protein Donor)
O3ANZLYS- 3543.17137.98H-Bond
(Protein Donor)
O2GNZLYS- 3542.83167.2H-Bond
(Protein Donor)
O1ANZLYS- 3542.760Ionic
(Protein Cationic)
O2GNZLYS- 3542.830Ionic
(Protein Cationic)
O4ND2ASN- 3583.22160.49H-Bond
(Protein Donor)
O2ANE2HIS- 3762.58165.4H-Bond
(Protein Donor)
O2ANZLYS- 3773.810Ionic
(Protein Cationic)
O2BNZLYS- 3772.570Ionic
(Protein Cationic)
O3BNZLYS- 3772.96162H-Bond
(Protein Donor)
O1GNZLYS- 5233.540Ionic
(Protein Cationic)
O3GNZLYS- 5232.710Ionic
(Protein Cationic)
O3GNZLYS- 5232.71167.24H-Bond
(Protein Donor)
O1BMG MG- 7021.850Metal Acceptor
O3GMG MG- 7021.890Metal Acceptor
O1BO3'GTP- 7022.6168.7H-Bond
(Protein Donor)
C5'C3'GTP- 7024.480Hydrophobic
C3'C1'GTP- 7024.390Hydrophobic