scPDB - 2w8y entry

Protein Data Bank Entry:

PDB ID : 2w8y

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2009-01-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	7.820	8.660	8.960	0.540	9.240	12

List of CHEMBLId :

CHEMBL1276308

Binding Site :

Uniprot Annotation

Name:	Progesterone receptor
ID:	PRGR_HUMAN
AC:	P06401
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	11.862
Number of residues:	42
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.722	432.000

% Hydrophobic	% Polar
67.97	32.03
According to VolSite

Ligand :

HET Code:	486
Formula:	C29H35NO2
Molecular weight:	429.594 g/mol
DrugBank ID:	DB00834
Buried Surface Area:	82.06 %
Polar Surface area:	40.54 Å2

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

Mass center Coordinates

X	Y	Z
10.481	4.58897	7.69766

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
C30	CD2	LEU- 715	3.61	0	Hydrophobic	false
C6	CD2	LEU- 718	4.29	0	Hydrophobic	false
C13	CB	LEU- 718	4.1	0	Hydrophobic	false
C32	CD1	LEU- 718	3.69	0	Hydrophobic	false
C26	CB	ASN- 719	4.32	0	Hydrophobic	false
C1	CD2	LEU- 721	3.64	0	Hydrophobic	false
C28	CB	GLU- 723	4.26	0	Hydrophobic	false
O30	NE2	GLN- 725	2.74	137.16	H-Bond (Protein Donor)	false
C29	CD2	LEU- 726	3.98	0	Hydrophobic	false
C29	CZ3	TRP- 755	3.89	0	Hydrophobic	false
C19	CE	MET- 756	3.67	0	Hydrophobic	false
C9	SD	MET- 756	3.83	0	Hydrophobic	false
C7	CB	MET- 759	4.09	0	Hydrophobic	false
C29	CE	MET- 759	4.32	0	Hydrophobic	false
C1	SD	MET- 759	4.46	0	Hydrophobic	false
C23	SD	MET- 759	3.51	0	Hydrophobic	false
C7	CB	VAL- 760	4.41	0	Hydrophobic	false
C32	CE2	PHE- 794	3.36	0	Hydrophobic	false
C32	CD2	LEU- 797	3.6	0	Hydrophobic	false
C30	CD2	LEU- 797	3.48	0	Hydrophobic	false
C16	CD2	LEU- 797	3.87	0	Hydrophobic	false
C8	SD	MET- 801	3.66	0	Hydrophobic	false
C15	CB	LEU- 887	4.06	0	Hydrophobic	false
C8	CD1	LEU- 887	4.44	0	Hydrophobic	false
C30	CE1	TYR- 890	3.58	0	Hydrophobic	false
C31	CD1	TYR- 890	3.75	0	Hydrophobic	false
C19	SG	CYS- 891	3.84	0	Hydrophobic	false
C16	CB	CYS- 891	4.15	0	Hydrophobic	false
C24	SD	MET- 909	3.93	0	Hydrophobic	false
C29	SD	MET- 909	3.65	0	Hydrophobic	false
C28	SD	MET- 909	3.85	0	Hydrophobic	false
C25	CG	MET- 909	4.01	0	Hydrophobic	false
C29	CG2	VAL- 912	3.7	0	Hydrophobic	false
O30	O	HOH- 2020	3.19	120.49	H-Bond (Protein Donor)	false