scPDB - 1y5r entry

Protein Data Bank Entry:

PDB ID : 1y5r

Resolution :3.000 Å

Experimental Method : X-ray

Deposition Date : 2004-12-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Corticosteroid 11-beta-dehydrogenase isozyme 1
ID:	DHI1_MOUSE
AC:	P50172
Organism:	Mus musculus
Reign:	Eukaryota
TaxID:	10090
EC Number:	1.1.1.146

Chains:

Chain Name:	Percentage of Residues within binding site
A	97 %
B	3 %

Ligand binding site composition:

B-Factor:	26.207
Number of residues:	31
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	NDP
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.544	934.875

% Hydrophobic	% Polar
54.87	45.13
According to VolSite

Ligand :

HET Code:	C0R
Formula:	C21H30O4
Molecular weight:	346.460 g/mol
DrugBank ID:	DB04652
Buried Surface Area:	71.02 %
Polar Surface area:	74.6 Å2

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

Mass center Coordinates

X	Y	Z
75.3479	49.2612	42.7101

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
C1	C4N	NDP- 1	4.16	0	Hydrophobic	false
C11	C4N	NDP- 1	3.44	0	Hydrophobic	false
C12	C3N	NDP- 1	3.44	0	Hydrophobic	false
C7	CD2	LEU- 126	4.06	0	Hydrophobic	false
C15	CD2	LEU- 126	3.8	0	Hydrophobic	false
O2	OG	SER- 170	3.1	170.03	H-Bond (Protein Donor)	false
C2	CD1	LEU- 171	3.87	0	Hydrophobic	false
C19	CB	ALA- 172	3.83	0	Hydrophobic	false
C19	CD1	ILE- 180	3.74	0	Hydrophobic	false
C11	CZ	TYR- 183	4.45	0	Hydrophobic	false
C18	CZ	TYR- 183	3.38	0	Hydrophobic	false
C19	CE2	TYR- 183	4.5	0	Hydrophobic	false
O2	OH	TYR- 183	2.81	131.61	H-Bond (Ligand Donor)	false
C9	CD1	LEU- 217	4.34	0	Hydrophobic	false
C1	CB	LEU- 217	4.34	0	Hydrophobic	false
C17	CB	ALA- 223	4.29	0	Hydrophobic	false
C16	CB	GLU- 226	3.77	0	Hydrophobic	false
C7	CG2	ILE- 227	3.84	0	Hydrophobic	false
C6	CD1	ILE- 231	3.98	0	Hydrophobic	false