scPDB - 2zb3 entry

Protein Data Bank Entry:

PDB ID : 2zb3

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2007-10-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Prostaglandin reductase 2
ID:	PTGR2_MOUSE
AC:	Q8VDQ1
Organism:	Mus musculus
Reign:	Eukaryota
TaxID:	10090
EC Number:	1.3.1.48

Chains:

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

Ligand binding site composition:

B-Factor:	25.168
Number of residues:	53
Including
Standard Amino Acids:	51
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.577	1154.250

% Hydrophobic	% Polar
48.83	51.17
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	61.63 %
Polar Surface area:	404.9 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
17.3274	0.519833	-73.5458

Binding mode :

What is Poseview ?

2D View
3D View

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
C5B	CG	PRO- 50	4.34	0	Hydrophobic	false
C3D	CB	PRO- 50	4.08	0	Hydrophobic	false
C5N	SD	MET- 135	3.64	0	Hydrophobic	false
C4N	CG2	THR- 139	3.45	0	Hydrophobic	false
O1A	N	ALA- 166	2.68	160.91	H-Bond (Protein Donor)	false
O1N	N	CYS- 167	2.72	177.86	H-Bond (Protein Donor)	false
C5N	SG	CYS- 167	4.07	0	Hydrophobic	false
O1X	N	GLY- 188	2.68	149.07	H-Bond (Protein Donor)	false
N3A	OH	TYR- 208	3.48	122.73	H-Bond (Protein Donor)	false
O2X	OH	TYR- 208	2.81	147.79	H-Bond (Protein Donor)	false
O3D	O	ASN- 231	3.04	165.71	H-Bond (Ligand Donor)	false
C4D	CB	ASN- 231	3.65	0	Hydrophobic	false
C3N	SG	CYS- 253	4	0	Hydrophobic	false
N7N	O	CYS- 253	2.92	165.22	H-Bond (Ligand Donor)	false
C1B	CG2	ILE- 256	4.11	0	Hydrophobic	false
C3D	CB	ILE- 256	4.43	0	Hydrophobic	false
C5B	CD1	ILE- 256	3.62	0	Hydrophobic	false
O2D	OH	TYR- 259	2.92	156.48	H-Bond (Protein Donor)	false
C3D	CE2	TYR- 259	4.44	0	Hydrophobic	false
N7N	O	PHE- 287	2.92	158.33	H-Bond (Ligand Donor)	false
O7N	N	VAL- 289	2.97	172.84	H-Bond (Protein Donor)	false
C4N	CG1	VAL- 289	4.33	0	Hydrophobic	false
C5B	SD	MET- 332	3.76	0	Hydrophobic	false
O1A	ND2	ASN- 337	3.34	129.55	H-Bond (Protein Donor)	false
O5B	ND2	ASN- 337	3.48	157.66	H-Bond (Protein Donor)	false
O3B	OD1	ASN- 337	2.77	157.73	H-Bond (Ligand Donor)	false
O2A	O	HOH- 458	2.6	156.3	H-Bond (Protein Donor)	false