scPDB - 3d90 entry

Protein Data Bank Entry:

PDB ID : 3d90

Resolution :2.260 Å

Experimental Method : X-ray

Deposition Date : 2008-05-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

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:	28.927
Number of residues:	35
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.773	398.250

% Hydrophobic	% Polar
72.03	27.97
According to VolSite

Ligand :

HET Code:	NOG
Formula:	C21H28O2
Molecular weight:	312.446 g/mol
DrugBank ID:	DB00367
Buried Surface Area:	77.96 %
Polar Surface area:	37.29 Å2

Number of
H-Bond Acceptors:	2
H-Bond Donors:	1
Rings:	4
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	1

Mass center Coordinates

X	Y	Z
-2.7227	-8.19213	25.6993

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
C20	CD2	LEU- 715	4.04	0	Hydrophobic	false
C1	CD2	LEU- 718	4.12	0	Hydrophobic	false
C21	CD1	LEU- 718	3.77	0	Hydrophobic	false
C11	CB	LEU- 718	3.79	0	Hydrophobic	false
C2	CD2	LEU- 721	3.35	0	Hydrophobic	false
C2	CG	GLN- 725	4.34	0	Hydrophobic	false
O3	NE2	GLN- 725	2.95	135.06	H-Bond (Protein Donor)	false
C18	CH2	TRP- 755	4.25	0	Hydrophobic	false
C18	CE	MET- 756	3.87	0	Hydrophobic	false
C8	SD	MET- 756	4.09	0	Hydrophobic	false
C15	SD	MET- 756	3.91	0	Hydrophobic	false
C2	SD	MET- 759	4.45	0	Hydrophobic	false
C6	CB	MET- 759	3.88	0	Hydrophobic	false
C10	SD	MET- 759	4.1	0	Hydrophobic	false
C6	CB	VAL- 760	4.25	0	Hydrophobic	false
C1	CD2	PHE- 778	4.48	0	Hydrophobic	false
C21	CE1	PHE- 794	4.06	0	Hydrophobic	false
C16	CD2	LEU- 797	3.94	0	Hydrophobic	false
C20	CD2	LEU- 797	4.17	0	Hydrophobic	false
C7	SD	MET- 801	3.86	0	Hydrophobic	false
C7	CD2	LEU- 887	4.37	0	Hydrophobic	false
C15	CB	LEU- 887	4.03	0	Hydrophobic	false
C16	CD1	TYR- 890	3.69	0	Hydrophobic	false
C20	CE1	TYR- 890	3.75	0	Hydrophobic	false
C16	CB	CYS- 891	3.78	0	Hydrophobic	false
C19	SG	CYS- 891	3.68	0	Hydrophobic	false
C19	CE2	PHE- 905	4.03	0	Hydrophobic	false