scPDB - 1o6y entry

Protein Data Bank Entry:

PDB ID : 1o6y

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2002-10-21

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 PknB
ID:	PKNB_MYCTU
AC:	P9WI81
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:	26.120
Number of residues:	39
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	2
Water Molecules:	2
Cofactors:
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
0.797	526.500

% Hydrophobic	% Polar
54.49	45.51
According to VolSite

Ligand :

HET Code:	ACP
Formula:	C11H14N5O12P3
Molecular weight:	501.176 g/mol
DrugBank ID:	DB03909
Buried Surface Area:	65.94 %
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
83.0216	77.9537	25.8635

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
C1'	CB	LEU- 17	4.34	0	Hydrophobic	false
O2G	N	GLY- 21	3.11	127.66	H-Bond (Protein Donor)	false
O3G	N	MET- 22	2.76	150.84	H-Bond (Protein Donor)	false
O3G	OG	SER- 23	3	164.09	H-Bond (Protein Donor)	false
C5'	CG2	VAL- 25	4.25	0	Hydrophobic	false
C1'	CB	VAL- 25	4.48	0	Hydrophobic	false
O2B	NZ	LYS- 40	2.6	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 40	3.07	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 40	3.07	134.37	H-Bond (Protein Donor)	false
O3A	NZ	LYS- 40	3.45	123	H-Bond (Protein Donor)	false
N6	O	GLU- 93	2.8	172.91	H-Bond (Ligand Donor)	false
N1	N	VAL- 95	3.07	161.02	H-Bond (Protein Donor)	false
C2'	CG2	THR- 99	4.26	0	Hydrophobic	false
O3'	O	ALA- 142	3.1	150.04	H-Bond (Ligand Donor)	false
C2'	SD	MET- 145	4.01	0	Hydrophobic	false
C3'	SD	MET- 155	4.2	0	Hydrophobic	false
O1B	MG	MG- 1280	2.09	0	Metal Acceptor	false
O1A	MG	MG- 1280	2.02	0	Metal Acceptor	false
O1G	MG	MG- 1281	2.08	0	Metal Acceptor	false
O2B	MG	MG- 1281	1.94	0	Metal Acceptor	false