scPDB - 5c93 entry

Protein Data Bank Entry:

PDB ID : 5c93

Resolution :2.520 Å

Experimental Method : X-ray

Deposition Date : 2015-06-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Two-component system histidine protein kinase
ID:	R9WYL1_LACPN
AC:	R9WYL1
Organism:	Lactobacillus plantarum 16
Reign:	Bacteria
TaxID:	1327988
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	61.974
Number of residues:	37
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.969	627.750

% Hydrophobic	% Polar
55.38	44.62
According to VolSite

Ligand :

HET Code:	ACP
Formula:	C11H14N5O12P3
Molecular weight:	501.176 g/mol
DrugBank ID:	DB03909
Buried Surface Area:	67.27 %
Polar Surface area:	310.64 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	3
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
4.29861	-16.0758	-31.9989

Binding mode :

What is Poseview ?

2D View
3D View

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
O1A	ND2	ASN- 510	3.27	155.65	H-Bond (Protein Donor)	false
O1A	ND2	ASN- 514	2.69	140.78	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 517	3.22	168.46	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 517	3.22	0	Ionic (Protein Cationic)	false
C2'	CZ	TYR- 518	3.48	0	Hydrophobic	false
C1'	CE2	TYR- 518	4.29	0	Hydrophobic	false
N6	OD2	ASP- 542	3.03	165.07	H-Bond (Ligand Donor)	false
C1'	CG1	VAL- 555	4.41	0	Hydrophobic	false
C4'	CD1	PHE- 560	3.85	0	Hydrophobic	false
C3'	CB	ARG- 561	4.37	0	Hydrophobic	false
O3'	N	VAL- 562	2.59	130.14	H-Bond (Protein Donor)	false
O2'	N	VAL- 562	3.45	130.63	H-Bond (Protein Donor)	false
C2'	CG1	VAL- 562	4.29	0	Hydrophobic	false
O1B	N	GLY- 574	2.78	138.37	H-Bond (Protein Donor)	false
O2B	N	GLY- 574	3.19	128.76	H-Bond (Protein Donor)	false
O2B	N	LEU- 575	3.16	120.46	H-Bond (Protein Donor)	false
O2B	N	GLY- 576	2.8	150.24	H-Bond (Protein Donor)	false
O2A	N	LEU- 577	2.79	157.34	H-Bond (Protein Donor)	false
C5'	CD1	LEU- 577	3.34	0	Hydrophobic	false
N1	O	HOH- 801	2.85	148.01	H-Bond (Protein Donor)	false