scPDB - 3bqd entry

Protein Data Bank Entry:

PDB ID : 3bqd

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2007-12-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glucocorticoid receptor
ID:	GCR_HUMAN
AC:	P04150
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:	62.515
Number of residues:	43
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.788	486.000

% Hydrophobic	% Polar
67.36	32.64
According to VolSite

Ligand :

HET Code:	DAY
Formula:	C30H36N2O4
Molecular weight:	488.618 g/mol
DrugBank ID:	-
Buried Surface Area:	78.82 %
Polar Surface area:	95.58 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	3
Rings:	6
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
39.8517	30.2947	9.33467

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
C21	CB	MET- 560	3.71	0	Hydrophobic	false
C11	CB	LEU- 563	3.87	0	Hydrophobic	false
O1	OD1	ASN- 564	2.63	160.25	H-Bond (Ligand Donor)	false
O4	ND2	ASN- 564	3.38	158.96	H-Bond (Protein Donor)	false
C22	CG	LEU- 566	3.39	0	Hydrophobic	false
C24	CG	GLN- 570	3.59	0	Hydrophobic	false
C19	CZ3	TRP- 600	4.37	0	Hydrophobic	false
C7	SD	MET- 601	3.7	0	Hydrophobic	false
C8	CE	MET- 601	4.34	0	Hydrophobic	false
C15	CE	MET- 601	4.18	0	Hydrophobic	false
C28	SD	MET- 601	4.38	0	Hydrophobic	false
C19	CG	MET- 604	4.02	0	Hydrophobic	false
C23	CG	MET- 604	4	0	Hydrophobic	false
C28	CB	MET- 604	3.95	0	Hydrophobic	false
C28	CB	ALA- 605	4.21	0	Hydrophobic	false
C26	CB	ALA- 607	3.65	0	Hydrophobic	false
C27	CD1	LEU- 608	4.41	0	Hydrophobic	false
C28	CD2	LEU- 608	4.22	0	Hydrophobic	false
C25	CB	LEU- 608	3.57	0	Hydrophobic	false
C29	CD	ARG- 611	4.25	0	Hydrophobic	false
C22	CD2	PHE- 623	3.66	0	Hydrophobic	false
C27	CB	PHE- 623	4.47	0	Hydrophobic	false
O2	OE1	GLN- 642	2.65	157.44	H-Bond (Ligand Donor)	false
C30	CB	GLN- 642	3.85	0	Hydrophobic	false
C7	CE	MET- 646	4.05	0	Hydrophobic	false
C28	SD	MET- 646	4.49	0	Hydrophobic	false
C14	CE	MET- 646	4.01	0	Hydrophobic	false
C15	CD2	LEU- 732	4.21	0	Hydrophobic	false
C30	CD2	LEU- 732	4.5	0	Hydrophobic	false
C16	CB	TYR- 735	3.84	0	Hydrophobic	false
C30	CG	TYR- 735	3.76	0	Hydrophobic	false
C18	SG	CYS- 736	4.06	0	Hydrophobic	false
C21	CG2	THR- 739	4.18	0	Hydrophobic	false
C18	CE2	PHE- 749	4.34	0	Hydrophobic	false