scPDB - 2zyt entry

Protein Data Bank Entry:

PDB ID : 2zyt

Resolution :1.550 Å

Experimental Method : X-ray

Deposition Date : 2009-01-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Sulfotransferase 1 family member D1
ID:	ST1D1_MOUSE
AC:	Q3UZZ6
Organism:	Mus musculus
Reign:	Eukaryota
TaxID:	10090
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
X	100 %

Ligand binding site composition:

B-Factor:	18.381
Number of residues:	39
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.331	381.375

% Hydrophobic	% Polar
51.33	48.67
According to VolSite

Ligand :

HET Code:	PPS
Formula:	C10H11N5O13P2S
Molecular weight:	503.233 g/mol
DrugBank ID:	DB02902
Buried Surface Area:	81.77 %
Polar Surface area:	315.29 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	2
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
19.3533	1.69594	10.9098

Binding mode :

What is Poseview ?

2D View
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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
OS1	NZ	LYS- 48	3.16	130.4	H-Bond (Protein Donor)	false
OS3	N	LYS- 48	2.93	153.35	H-Bond (Protein Donor)	false
O6P	NZ	LYS- 48	2.91	159.65	H-Bond (Protein Donor)	false
OS1	NZ	LYS- 48	3.16	0	Ionic (Protein Cationic)	false
O5P	N	GLY- 50	3.14	154.07	H-Bond (Protein Donor)	false
O5P	OG1	THR- 51	2.62	151.49	H-Bond (Protein Donor)	false
O5P	N	THR- 51	2.83	158.05	H-Bond (Protein Donor)	false
O4P	OG1	THR- 52	2.68	156.94	H-Bond (Protein Donor)	false
O4P	N	THR- 52	2.91	164.81	H-Bond (Protein Donor)	false
DuAr	DuAr	TRP- 53	3.83	0	Aromatic Face/Face	false
OS2	NZ	LYS- 106	3.16	149.01	H-Bond (Protein Donor)	false
OS2	NZ	LYS- 106	3.16	0	Ionic (Protein Cationic)	false
O3'	NH1	ARG- 130	3.16	152.46	H-Bond (Protein Donor)	false
O3P	NH2	ARG- 130	2.89	149.35	H-Bond (Protein Donor)	false
O3P	NH1	ARG- 130	3.29	132.03	H-Bond (Protein Donor)	false
O3P	CZ	ARG- 130	3.51	0	Ionic (Protein Cationic)	false
O3'	OG	SER- 138	3.47	134.05	H-Bond (Protein Donor)	false
O1P	OG	SER- 138	2.73	157.03	H-Bond (Protein Donor)	false
C1'	CE1	TYR- 193	4.26	0	Hydrophobic	false
N3	OH	TYR- 193	2.87	132.14	H-Bond (Protein Donor)	false
N6	O	SER- 227	2.81	130.23	H-Bond (Ligand Donor)	false
C5'	CE2	PHE- 255	4.16	0	Hydrophobic	false
O2'	N	ARG- 257	3.29	148.75	H-Bond (Protein Donor)	false
O1P	NE	ARG- 257	2.88	162.73	H-Bond (Protein Donor)	false
O3P	NH2	ARG- 257	3.28	143.8	H-Bond (Protein Donor)	false
O1P	CZ	ARG- 257	3.67	0	Ionic (Protein Cationic)	false
O2P	N	LYS- 258	2.84	162.07	H-Bond (Protein Donor)	false
O2P	N	GLY- 259	2.8	161.75	H-Bond (Protein Donor)	false
OS1	O	HOH- 2040	2.61	179.97	H-Bond (Protein Donor)	false