scPDB - 3q2k entry

Protein Data Bank Entry:

PDB ID : 3q2k

Resolution :2.130 Å

Experimental Method : X-ray

Deposition Date : 2010-12-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Probable oxidoreductase
ID:	Q79H45_BORPE
AC:	Q79H45
Organism:	Bordetella pertussis
Reign:	Bacteria
TaxID:	257313
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	41.242
Number of residues:	32
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	NAI
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.399	1140.750

% Hydrophobic	% Polar
32.84	67.16
According to VolSite

Ligand :

HET Code:	HP7
Formula:	C17H22N3O18P2
Molecular weight:	618.313 g/mol
DrugBank ID:	-
Buried Surface Area:	43.77 %
Polar Surface area:	345.59 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	3
Aromatic rings:	0
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
104.521	55.9026	58.4713

Binding mode :

What is Poseview ?

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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
O2A	NH2	ARG- 20	2.85	152.84	H-Bond (Protein Donor)	false
O2A	NH1	ARG- 20	3.16	136.87	H-Bond (Protein Donor)	false
O2B	NH1	ARG- 20	2.86	136.83	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 20	3.44	0	Ionic (Protein Cationic)	false
O2B	CZ	ARG- 20	3.87	0	Ionic (Protein Cationic)	false
O3'	NZ	LYS- 103	2.62	174.26	H-Bond (Protein Donor)	false
O'P	NE	ARG- 164	2.72	142.98	H-Bond (Protein Donor)	false
O'P	NH1	ARG- 164	2.88	131.97	H-Bond (Protein Donor)	false
O'P	CZ	ARG- 164	3.18	0	Ionic (Protein Cationic)	false
C1C	CD	ARG- 164	3.91	0	Hydrophobic	false
C4C	CD	ARG- 164	4.27	0	Hydrophobic	false
O'Q	OH	TYR- 168	2.57	150.53	H-Bond (Protein Donor)	false
C4C	CD1	TYR- 168	3.91	0	Hydrophobic	false
C5C	CE1	TYR- 168	4.36	0	Hydrophobic	false
O4'	OD1	ASN- 187	2.74	165.41	H-Bond (Ligand Donor)	false
O'P	NE2	GLN- 188	3.1	162.46	H-Bond (Protein Donor)	false
O3'	NE2	HIS- 191	2.61	140.63	H-Bond (Ligand Donor)	false
O4	N	ASN- 247	2.85	160.67	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 287	3.21	0	Ionic (Protein Cationic)	false
O2B	CZ	ARG- 287	3.48	0	Ionic (Protein Cationic)	false
C1'	C4N	NAI- 500	4.44	0	Hydrophobic	false
C3'	C4N	NAI- 500	3.33	0	Hydrophobic	false
N2'	O7N	NAI- 500	2.69	166.59	H-Bond (Ligand Donor)	false