scPDB - 4r39 entry

Protein Data Bank Entry:

PDB ID : 4r39

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2014-08-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Blue-light-activated histidine kinase 2
ID:	LVHK2_ERYLH
AC:	Q2NB77
Organism:	Erythrobacter litoralis
Reign:	Bacteria
TaxID:	314225
EC Number:	2.7.13.3

Chains:

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

Ligand binding site composition:

B-Factor:	26.149
Number of residues:	35
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.316	462.375

% Hydrophobic	% Polar
42.34	57.66
According to VolSite

Ligand :

HET Code:	ANP
Formula:	C10H13N6O12P3
Molecular weight:	502.164 g/mol
DrugBank ID:	-
Buried Surface Area:	63.86 %
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
61.5715	27.6631	71.6327

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
O3G	OG	SER- 171	2.54	156.39	H-Bond (Protein Donor)	false
O1G	NH2	ARG- 175	3.31	149.9	H-Bond (Protein Donor)	false
O1A	ND2	ASN- 250	3.01	145.19	H-Bond (Protein Donor)	false
O2B	NE2	HIS- 254	2.91	153.54	H-Bond (Protein Donor)	false
C2'	CB	HIS- 254	4.08	0	Hydrophobic	false
N6	OD2	ASP- 282	2.84	154.02	H-Bond (Ligand Donor)	false
C1'	CG2	ILE- 287	4.47	0	Hydrophobic	false
O2A	NE1	TRP- 293	3.42	125.23	H-Bond (Protein Donor)	false
O1B	ND2	ASN- 298	2.8	136.93	H-Bond (Protein Donor)	false
O2A	N	ASN- 298	3	148.63	H-Bond (Protein Donor)	false
O3A	ND2	ASN- 298	3.37	120.41	H-Bond (Protein Donor)	false
O1G	N	GLY- 300	3.09	140	H-Bond (Protein Donor)	false
O2G	MG	MG- 401	1.99	0	Metal Acceptor	false
O2B	MG	MG- 401	2.16	0	Metal Acceptor	false
O1A	MG	MG- 401	2.1	0	Metal Acceptor	false