scPDB - 3ebl entry

Protein Data Bank Entry:

PDB ID : 3ebl

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2008-08-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Gibberellin receptor GID1
ID:	GID1_ORYSJ
AC:	Q6L545
Organism:	Oryza sativa subsp. japonica
Reign:	Eukaryota
TaxID:	39947
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	24.498
Number of residues:	36
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.498	428.625

% Hydrophobic	% Polar
46.46	53.54
According to VolSite

Ligand :

HET Code:	GA4
Formula:	C19H23O5
Molecular weight:	331.383 g/mol
DrugBank ID:	DB07815
Buried Surface Area:	78.24 %
Polar Surface area:	86.66 Å2

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

Mass center Coordinates

X	Y	Z
18.8245	56.0575	-28.0181

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
C2	CD1	ILE- 24	4.38	0	Hydrophobic	false
C11	CG2	ILE- 24	3.67	0	Hydrophobic	false
C1	CG	PHE- 27	3.45	0	Hydrophobic	false
C2	CD2	PHE- 27	3.84	0	Hydrophobic	false
C11	CB	PHE- 27	4.33	0	Hydrophobic	false
C12	CB	LYS- 28	4.18	0	Hydrophobic	false
C1	CE2	TYR- 31	4.24	0	Hydrophobic	false
C9	CE2	TYR- 31	4.3	0	Hydrophobic	false
C15	CD2	TYR- 31	4.09	0	Hydrophobic	false
O71	N	GLY- 122	3.1	123.76	H-Bond (Protein Donor)	false
O71	OG	SER- 123	2.8	167.2	H-Bond (Protein Donor)	false
C3	CD1	ILE- 133	3.74	0	Hydrophobic	false
C3	CZ	TYR- 134	4.29	0	Hydrophobic	false
O31	OH	TYR- 134	2.73	170.55	H-Bond (Ligand Donor)	false
O71	OG	SER- 198	3.11	122.85	H-Bond (Protein Donor)	false
O72	OG	SER- 198	2.9	172.13	H-Bond (Protein Donor)	false
C18	CB	SER- 198	3.89	0	Hydrophobic	false
C12	CB	PHE- 245	4.42	0	Hydrophobic	false
C14	CG2	VAL- 246	3.78	0	Hydrophobic	false
C3	CD1	LEU- 330	3.95	0	Hydrophobic	false