scPDB - 3w9r entry

Protein Data Bank Entry:

PDB ID : 3w9r

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2013-04-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Abscisic acid receptor PYL9
ID:	PYL9_ARATH
AC:	Q84MC7
Organism:	Arabidopsis thaliana
Reign:	Eukaryota
TaxID:	3702
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	29.891
Number of residues:	30
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.147	617.625

% Hydrophobic	% Polar
62.30	37.70
According to VolSite

Ligand :

HET Code:	A8S
Formula:	C15H19O4
Molecular weight:	263.309 g/mol
DrugBank ID:	-
Buried Surface Area:	60.67 %
Polar Surface area:	77.43 Å2

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

Mass center Coordinates

X	Y	Z
37.8779	-45.2985	-7.54105

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
O11	NZ	LYS- 63	3.13	154.54	H-Bond (Protein Donor)	false
O12	NZ	LYS- 63	2.78	142.46	H-Bond (Protein Donor)	false
O11	NZ	LYS- 63	3.13	0	Ionic (Protein Cationic)	false
O12	NZ	LYS- 63	2.78	0	Ionic (Protein Cationic)	false
C13	CB	PHE- 65	3.9	0	Hydrophobic	false
C13	CG1	VAL- 85	4.22	0	Hydrophobic	false
C14	CG1	VAL- 85	3.75	0	Hydrophobic	false
C13	CD1	LEU- 89	4.11	0	Hydrophobic	false
C11	CB	ALA- 91	4.24	0	Hydrophobic	false
C14	CB	ALA- 91	3.64	0	Hydrophobic	false
C14	CB	SER- 94	4.11	0	Hydrophobic	false
C15	CB	SER- 94	3.8	0	Hydrophobic	false
C15	CD1	ILE- 112	3.73	0	Hydrophobic	false
C11	CB	HIS- 117	3.83	0	Hydrophobic	false
C14	CB	HIS- 117	4.39	0	Hydrophobic	false
C6	CD1	LEU- 119	3.89	0	Hydrophobic	false
C11	CD1	LEU- 119	3.98	0	Hydrophobic	false
C15	CD1	LEU- 119	4.41	0	Hydrophobic	false
C6	CE1	TYR- 122	3.92	0	Hydrophobic	false
C6	CG1	VAL- 162	4.24	0	Hydrophobic	false
C6	CD1	LEU- 165	3.87	0	Hydrophobic	false
C7	CD1	LEU- 165	4.49	0	Hydrophobic	false
C13	CD2	LEU- 165	3.79	0	Hydrophobic	false
O11	ND2	ASN- 169	3.28	132.03	H-Bond (Protein Donor)	false
O12	O	HOH- 301	2.75	135.55	H-Bond (Protein Donor)	false
O10	O	HOH- 312	2.74	156.91	H-Bond (Protein Donor)	false