scPDB - 4gyz entry

Protein Data Bank Entry:

PDB ID : 4gyz

Resolution :2.560 Å

Experimental Method : X-ray

Deposition Date : 2012-09-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Tyrosyl-DNA phosphodiesterase 2
ID:	TYDP2_MOUSE
AC:	Q9JJX7
Organism:	Mus musculus
Reign:	Eukaryota
TaxID:	10090
EC Number:	3.1.4

Chains:

Chain Name:	Percentage of Residues within binding site
A	64 %
B	36 %

Ligand binding site composition:

B-Factor:	41.450
Number of residues:	36
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
1.070	1356.750

% Hydrophobic	% Polar
40.80	59.20
According to VolSite

Ligand :

HET Code:	D5M
Formula:	C10H12N5O6P
Molecular weight:	329.206 g/mol
DrugBank ID:	-
Buried Surface Area:	66.81 %
Polar Surface area:	181.31 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	2
Rings:	3
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
21.227	77.8335	47.9886

Binding mode :

What is Poseview ?

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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
N6	O	SER- 148	3.33	131.72	H-Bond (Ligand Donor)	false
O3P	NE2	HIS- 236	2.89	138.48	H-Bond (Protein Donor)	false
O3P	OG	SER- 239	2.73	172.3	H-Bond (Protein Donor)	false
O2P	OD2	ASP- 272	2.63	155.5	H-Bond (Protein Donor)	false
O2P	ND2	ASN- 274	3.2	125.15	H-Bond (Protein Donor)	false
C5'	CE2	TRP- 307	3.96	0	Hydrophobic	false
C4'	CZ2	TRP- 307	3.56	0	Hydrophobic	false
C3'	CE2	PHE- 325	4.08	0	Hydrophobic	false
O1P	NE2	HIS- 359	2.96	158.17	H-Bond (Protein Donor)	false
O2P	NE2	HIS- 359	3.29	120.63	H-Bond (Protein Donor)	false
O1P	MG	MG- 402	2.31	0	Metal Acceptor	false