scPDB - 4y12 entry

Protein Data Bank Entry:

PDB ID : 4y12

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2015-02-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Serine/threonine-protein kinase PknG
ID:	PKNG_MYCTU
AC:	P9WI73
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	2.7.11.1

Chains:

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

Ligand binding site composition:

B-Factor:	41.273
Number of residues:	37
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	2
Water Molecules:	2
Cofactors:
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
0.603	560.250

% Hydrophobic	% Polar
47.59	52.41
According to VolSite

Ligand :

HET Code:	AGS
Formula:	C10H14N5O12P3S
Molecular weight:	521.231 g/mol
DrugBank ID:	DB02930
Buried Surface Area:	56.72 %
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
-0.841355	7.49419	-29.5355

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
C1'	CG2	ILE- 157	3.92	0	Hydrophobic	false
C4'	CB	ALA- 158	4.09	0	Hydrophobic	false
C1'	CB	ALA- 158	4.42	0	Hydrophobic	false
O1B	N	GLY- 161	2.78	128.02	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 181	2.54	168.78	H-Bond (Protein Donor)	false
O3G	NZ	LYS- 181	3.18	127.35	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 181	2.75	160.83	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 181	2.54	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 181	3.18	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 181	2.75	0	Ionic (Protein Cationic)	false
N6	O	GLU- 233	2.88	156.79	H-Bond (Ligand Donor)	false
N1	N	VAL- 235	2.84	168.4	H-Bond (Protein Donor)	false
C2'	CE	MET- 283	4.07	0	Hydrophobic	false
C3'	CD1	ILE- 292	3.72	0	Hydrophobic	false
O2A	MG	MG- 503	2.2	0	Metal Acceptor	false
O2G	MG	MG- 504	2.03	0	Metal Acceptor	false
O1B	O	HOH- 676	2.75	167.73	H-Bond (Protein Donor)	false