scPDB - 1rpw entry

Protein Data Bank Entry:

PDB ID : 1rpw

Resolution :2.900 Å

Experimental Method : X-ray

Deposition Date : 2003-12-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	HTH-type transcriptional regulator QacR
ID:	QACR_STAAU
AC:	P0A0N4
Organism:	Staphylococcus aureus
Reign:	Bacteria
TaxID:	1280
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	9 %
B	91 %

Ligand binding site composition:

B-Factor:	55.870
Number of residues:	33
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.316	1002.375

% Hydrophobic	% Polar
53.87	46.13
According to VolSite

Ligand :

HET Code:	DID
Formula:	C20H28N4O2
Molecular weight:	356.462 g/mol
DrugBank ID:	DB03808
Buried Surface Area:	50.64 %
Polar Surface area:	121.68 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	4
Rings:	2
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	2
Rule of Five Violation:	0
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
-66.1146	-44.5916	4.44108

Binding mode :

What is Poseview ?

2D View
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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
C6'	CB	GLU- 57	4.47	0	Hydrophobic	false
C7'	CE3	TRP- 61	3.44	0	Hydrophobic	false
C6'	CB	TRP- 61	3.96	0	Hydrophobic	false
C9	OE1	GLU- 120	3.81	0	Ionic (Ligand Cationic)	false
C9	OE2	GLU- 120	4	0	Ionic (Ligand Cationic)	false
N1	OE2	GLU- 120	2.92	152.66	H-Bond (Ligand Donor)	false
C5	CB	GLU- 120	3.22	0	Hydrophobic	false
C6	CB	TYR- 123	4.24	0	Hydrophobic	false
C7	CG	TYR- 123	4.23	0	Hydrophobic	false
C10	CE2	TYR- 123	4.1	0	Hydrophobic	false
C8'	CE2	TYR- 123	4.16	0	Hydrophobic	false
C2	CB	ASN- 157	3.39	0	Hydrophobic	false
C3	CB	PHE- 162	4.07	0	Hydrophobic	false