scPDB - 4apu entry

Protein Data Bank Entry:

PDB ID : 4apu

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2012-04-06

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:	35.378
Number of residues:	36
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.409	324.000

% Hydrophobic	% Polar
66.67	33.33
According to VolSite

Ligand :

HET Code:	OR8
Formula:	C17H19ClN4O3S
Molecular weight:	394.876 g/mol
DrugBank ID:	-
Buried Surface Area:	85.93 %
Polar Surface area:	98.4 Å2

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

Mass center Coordinates

X	Y	Z
-1.00846	14.6324	9.74181

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
CL	CD2	LEU- 715	3.28	0	Hydrophobic	false
CL	CB	LEU- 718	3.39	0	Hydrophobic	false
C26	CD1	LEU- 718	3.94	0	Hydrophobic	false
C1	CB	LEU- 718	4.08	0	Hydrophobic	false
N13	OD1	ASN- 719	2.96	146.74	H-Bond (Ligand Donor)	false
C23	CG	LEU- 721	3.69	0	Hydrophobic	false
C12	CH2	TRP- 755	4.03	0	Hydrophobic	false
C4	CZ3	TRP- 755	3.42	0	Hydrophobic	false
C24	SD	MET- 756	3.33	0	Hydrophobic	false
C22	SD	MET- 756	4.49	0	Hydrophobic	false
C4	SD	MET- 756	3.74	0	Hydrophobic	false
C23	SD	MET- 759	4.41	0	Hydrophobic	false
C3	SD	MET- 759	4.1	0	Hydrophobic	false
C22	CB	VAL- 760	4.36	0	Hydrophobic	false
C26	CE1	PHE- 778	3.91	0	Hydrophobic	false
C26	CE1	PHE- 794	4.29	0	Hydrophobic	false
C26	CD2	LEU- 797	4.17	0	Hydrophobic	false
C26	CE	MET- 801	3.68	0	Hydrophobic	false
C22	SD	MET- 801	3.7	0	Hydrophobic	false
C24	CB	LEU- 887	3.99	0	Hydrophobic	false
C22	CD2	LEU- 887	4.5	0	Hydrophobic	false
C24	CB	CYS- 891	3.79	0	Hydrophobic	false
C12	SG	CYS- 891	3.76	0	Hydrophobic	false
C12	SD	MET- 909	3.77	0	Hydrophobic	false
C5	CE	MET- 909	4.08	0	Hydrophobic	false