scPDB - 4jrn entry

Protein Data Bank Entry:

PDB ID : 4jrn

Resolution :2.710 Å

Experimental Method : X-ray

Deposition Date : 2013-03-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Rhoptry kinase family protein
ID:	Q2PAY2_TOXGO
AC:	Q2PAY2
Organism:	Toxoplasma gondii
Reign:	Eukaryota
TaxID:	5811
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	50.611
Number of residues:	33
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
0.205	580.500

% Hydrophobic	% Polar
44.77	55.23
According to VolSite

Ligand :

HET Code:	ANP
Formula:	C10H13N6O12P3
Molecular weight:	502.164 g/mol
DrugBank ID:	-
Buried Surface Area:	56.25 %
Polar Surface area:	322.68 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
6.59387	46.3388	18.9386

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
O2G	N	GLY- 262	3.01	147.68	H-Bond (Protein Donor)	false
C1'	CG2	VAL- 266	4.19	0	Hydrophobic	false
C5'	CG2	VAL- 266	4.01	0	Hydrophobic	false
O2B	NZ	LYS- 281	3.25	152.08	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 281	3.25	0	Ionic (Protein Cationic)	false
N6	O	MET- 357	3.11	167.88	H-Bond (Ligand Donor)	false
N1	N	ALA- 359	2.98	167.48	H-Bond (Protein Donor)	false
O2'	OD2	ASP- 362	3.06	161.16	H-Bond (Ligand Donor)	false
O1G	MG	MG- 603	2.46	0	Metal Acceptor	false
O3G	MG	MG- 603	2.02	0	Metal Acceptor	false
O2B	MG	MG- 603	2.65	0	Metal Acceptor	false