scPDB - 3zra entry

Protein Data Bank Entry:

PDB ID : 3zra

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2011-06-15

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
B	100 %

Ligand binding site composition:

B-Factor:	28.034
Number of residues:	33
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.735	381.375

% Hydrophobic	% Polar
73.45	26.55
According to VolSite

Ligand :

HET Code:	ORB
Formula:	C18H17ClFN3O3S
Molecular weight:	409.862 g/mol
DrugBank ID:	-
Buried Surface Area:	80.03 %
Polar Surface area:	93.47 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
3.25319	14.5267	-24.4759

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
C13	CD2	LEU- 715	4.15	0	Hydrophobic	false
C25	CB	LEU- 715	3.39	0	Hydrophobic	false
CL2	CD2	LEU- 718	3.92	0	Hydrophobic	false
C11	CD1	LEU- 718	4.32	0	Hydrophobic	false
C8	CB	LEU- 718	3.93	0	Hydrophobic	false
C9	CB	LEU- 718	3.62	0	Hydrophobic	false
N14	OD1	ASN- 719	2.77	151.26	H-Bond (Ligand Donor)	false
CL2	CD2	LEU- 721	3.71	0	Hydrophobic	false
C24	CH2	TRP- 755	4.09	0	Hydrophobic	false
C23	SD	MET- 756	4.31	0	Hydrophobic	false
C8	CE	MET- 759	4.39	0	Hydrophobic	false
C4	CE	MET- 759	3.92	0	Hydrophobic	false
F2	CG2	VAL- 760	3.27	0	Hydrophobic	false
C2	CB	VAL- 760	4.24	0	Hydrophobic	false
F2	CD2	LEU- 763	4.23	0	Hydrophobic	false
CL2	CD1	PHE- 778	3.99	0	Hydrophobic	false
C11	CD2	LEU- 797	4.34	0	Hydrophobic	false
C23	CD2	LEU- 797	3.88	0	Hydrophobic	false
F2	SD	MET- 801	3.38	0	Hydrophobic	false
F2	CD2	LEU- 887	3.58	0	Hydrophobic	false
C23	CD1	TYR- 890	4.08	0	Hydrophobic	false
C24	SG	CYS- 891	4.26	0	Hydrophobic	false
C24	CE2	PHE- 905	4.15	0	Hydrophobic	false
C24	CE	MET- 909	3.35	0	Hydrophobic	false