scPDB - 4bzc entry

Protein Data Bank Entry:

PDB ID : 4bzc

Resolution :2.880 Å

Experimental Method : X-ray

Deposition Date : 2013-07-25

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	22 %
B	30 %
D	48 %

Ligand binding site composition:

B-Factor:	58.060
Number of residues:	29
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	2
Water Molecules:	1
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.656	1657.125

% Hydrophobic	% Polar
36.86	63.14
According to VolSite

Ligand :

HET Code:	T8T
Formula:	C10H12N5O12P3S
Molecular weight:	519.215 g/mol
DrugBank ID:	-
Buried Surface Area:	64.02 %
Polar Surface area:	312.16 Å2

Number of
H-Bond Acceptors:	17
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

X	Y	Z
46.7835	29.8761	36.4664

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
O3'	N	ASN- 119	3.17	178.52	H-Bond (Protein Donor)	false
C1'	CB	ASN- 119	3.57	0	Hydrophobic	false
O3'	O	VAL- 156	2.57	148.25	H-Bond (Ligand Donor)	false
C2'	CG1	VAL- 156	3.51	0	Hydrophobic	false
C1'	CE2	PHE- 157	3.38	0	Hydrophobic	false
C2'	CZ	PHE- 157	3.35	0	Hydrophobic	false
DuAr	CZ	ARG- 333	3.59	165.29	Pi/Cation	false
O1G	CZ	ARG- 352	3.72	0	Ionic (Protein Cationic)	false
O1G	NH1	ARG- 352	2.9	158.21	H-Bond (Protein Donor)	false
O2G	NH2	ARG- 352	3.41	164.31	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 354	3.67	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 354	2.98	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 354	2.98	169.25	H-Bond (Protein Donor)	false
O6	NE	ARG- 372	3.34	120.5	H-Bond (Protein Donor)	false
O2A	NE2	HIS- 376	2.81	151.56	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 377	3.9	0	Ionic (Protein Cationic)	false
O2G	NZ	LYS- 377	3.3	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 377	3.56	0	Ionic (Protein Cationic)	false
O2G	NZ	LYS- 377	3.3	149.43	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 523	3.82	0	Ionic (Protein Cationic)	false
O2G	NZ	LYS- 523	3.86	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 523	3.03	0	Ionic (Protein Cationic)	false
O2B	MG	MG- 950	2.34	0	Metal Acceptor	false
O3G	MG	MG- 950	2.16	0	Metal Acceptor	false