scPDB - 2vna entry

Protein Data Bank Entry:

PDB ID : 2vna

Resolution :2.170 Å

Experimental Method : X-ray

Deposition Date : 2008-02-01

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_HUMAN
AC:	Q8N8N7
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.3.1.48

Chains:

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

Ligand binding site composition:

B-Factor:	38.958
Number of residues:	54
Including
Standard Amino Acids:	51
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.366	2193.750

% Hydrophobic	% Polar
54.46	45.54
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	63.24 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
24.3382	-11.4029	-20.0782

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	4.28	0	Hydrophobic	false
C5D	CG	PRO- 50	4.17	0	Hydrophobic	false
C2D	CB	PRO- 50	3.98	0	Hydrophobic	false
C5N	SD	MET- 135	3.6	0	Hydrophobic	false
C5N	CG2	THR- 139	4.12	0	Hydrophobic	false
O1N	N	CYS- 167	2.69	159.53	H-Bond (Protein Donor)	false
C5N	SG	CYS- 167	3.95	0	Hydrophobic	false
O3X	N	GLY- 188	2.81	129.21	H-Bond (Protein Donor)	false
O2X	NZ	LYS- 192	2.79	156.49	H-Bond (Protein Donor)	false
O2X	NZ	LYS- 192	2.79	0	Ionic (Protein Cationic)	false
O3X	NZ	LYS- 192	3.9	0	Ionic (Protein Cationic)	false
O3D	O	ASN- 231	2.84	163.17	H-Bond (Ligand Donor)	false
C4D	CB	ASN- 231	3.57	0	Hydrophobic	false
N7N	O	CYS- 253	3.08	154.94	H-Bond (Ligand Donor)	false
C1B	CG2	ILE- 256	4.15	0	Hydrophobic	false
C3D	CB	ILE- 256	4.27	0	Hydrophobic	false
C5B	CD1	ILE- 256	3.61	0	Hydrophobic	false
O2D	OH	TYR- 259	2.88	164.08	H-Bond (Protein Donor)	false
C3D	CE2	TYR- 259	4.26	0	Hydrophobic	false
N7N	O	PHE- 287	2.71	162.96	H-Bond (Ligand Donor)	false
O7N	N	VAL- 289	3.01	169.26	H-Bond (Protein Donor)	false
C5B	SD	MET- 332	3.77	0	Hydrophobic	false
O1A	ND2	ASN- 337	3.03	127.75	H-Bond (Protein Donor)	false
O5B	ND2	ASN- 337	3.4	148.95	H-Bond (Protein Donor)	false
O2A	O	HOH- 2082	2.55	159.16	H-Bond (Protein Donor)	false
O3B	O	HOH- 2086	2.78	147.09	H-Bond (Protein Donor)	false