scPDB - 2y05 entry

Protein Data Bank Entry:

PDB ID : 2y05

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2010-11-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Prostaglandin reductase 1
ID:	PTGR1_HUMAN
AC:	Q14914
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	90 %
B	10 %

Ligand binding site composition:

B-Factor:	21.616
Number of residues:	25
Including
Standard Amino Acids:	20
Non Standard Amino Acids:	4
Water Molecules:	1
Cofactors:	NAP
Metals:	CL CL

Cavity properties

Ligandability	Volume (Å3)
1.216	921.375

% Hydrophobic	% Polar
45.05	54.95
According to VolSite

Ligand :

HET Code:	RAL
Formula:	C28H28NO4S
Molecular weight:	474.591 g/mol
DrugBank ID:	DB00481
Buried Surface Area:	41.02 %
Polar Surface area:	99.44 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	3
Rings:	5
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
43.9891	48.7543	18.1724

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
C18	CB	TYR- 49	4.22	0	Hydrophobic	false
C24	CE1	TYR- 49	4.35	0	Hydrophobic	false
C3	CB	TYR- 49	3.37	0	Hydrophobic	false
S6	CB	VAL- 52	3.85	0	Hydrophobic	false
C8	CG1	VAL- 52	4	0	Hydrophobic	false
O11	NE	ARG- 56	2.92	170.17	H-Bond (Protein Donor)	false
C24	CG1	VAL- 77	3.71	0	Hydrophobic	false
C10	CG2	VAL- 77	3.87	0	Hydrophobic	false
C22	CG2	VAL- 77	3.29	0	Hydrophobic	false
C20	CG1	VAL- 77	3.3	0	Hydrophobic	false
C30	CB	SER- 88	3.87	0	Hydrophobic	false
C22	CG1	VAL- 271	4.02	0	Hydrophobic	false
C24	CE2	TYR- 273	4.19	0	Hydrophobic	false
C28	CE1	TYR- 273	3.6	0	Hydrophobic	false
C3	C2D	NAP- 701	4.32	0	Hydrophobic	false