scPDB - 4rf9 entry

Protein Data Bank Entry:

PDB ID : 4rf9

Resolution :2.350 Å

Experimental Method : X-ray

Deposition Date : 2014-09-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Arginine kinase
ID:	KARG_ANTJA
AC:	O15992
Organism:	Anthopleura japonica
Reign:	Eukaryota
TaxID:	67755
EC Number:	2.7.3.3

Chains:

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

Ligand binding site composition:

B-Factor:	43.232
Number of residues:	24
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.593	924.750

% Hydrophobic	% Polar
35.77	64.23
According to VolSite

Ligand :

HET Code:	AGS
Formula:	C10H14N5O12P3S
Molecular weight:	521.231 g/mol
DrugBank ID:	DB02930
Buried Surface Area:	41.7 %
Polar Surface area:	329.24 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
7.53332	35.1265	112.481

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
N1	OG	SER- 126	3.2	165.75	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 128	3.57	0	Ionic (Protein Cationic)	false
O1A	NH2	ARG- 128	2.79	150.05	H-Bond (Protein Donor)	false
C1'	CD	ARG- 128	4.41	0	Hydrophobic	false
O1A	NE	ARG- 130	3.32	173.32	H-Bond (Protein Donor)	false
O2A	NH2	ARG- 130	3.25	170.89	H-Bond (Protein Donor)	false
O1A	NH2	ARG- 233	2.91	126.53	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 233	3.89	0	Ionic (Protein Cationic)	false
N7	OG	SER- 286	2.77	164.63	H-Bond (Protein Donor)	false
DuAr	DuAr	HIS- 288	3.87	0	Aromatic Face/Face	false
O2G	NH2	ARG- 802	2.67	160.29	H-Bond (Protein Donor)	false
O2G	CZ	ARG- 802	3.66	0	Ionic (Protein Cationic)	false