scPDB - 3f69 entry

Protein Data Bank Entry:

PDB ID : 3f69

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2008-11-05

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:	23.989
Number of residues:	29
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.253	1117.125

% Hydrophobic	% Polar
44.41	55.59
According to VolSite

Ligand :

HET Code:	XDR
Formula:	C32H29N3O5
Molecular weight:	535.590 g/mol
DrugBank ID:	-
Buried Surface Area:	63.94 %
Polar Surface area:	95.05 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	1
Rings:	8
Aromatic rings:	5
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
-46.764	-46.1275	5.44589

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
CBH	CB	LEU- 17	4.42	0	Hydrophobic	false
CAK	CD1	LEU- 17	3.79	0	Hydrophobic	false
CAG	CD2	LEU- 17	3.98	0	Hydrophobic	false
CBG	CD1	LEU- 17	4.15	0	Hydrophobic	false
CBD	CB	LEU- 17	3.85	0	Hydrophobic	false
CAB	CG2	VAL- 25	4.31	0	Hydrophobic	false
CBI	CG2	VAL- 25	4.24	0	Hydrophobic	false
CBF	CG1	VAL- 25	4.07	0	Hydrophobic	false
CBE	CG2	VAL- 25	3.68	0	Hydrophobic	false
CAF	CD	LYS- 40	4.01	0	Hydrophobic	false
CAJ	SD	MET- 92	3.79	0	Hydrophobic	false
NAU	O	GLU- 93	2.82	174.09	H-Bond (Ligand Donor)	false
OAC	N	VAL- 95	2.91	154.67	H-Bond (Protein Donor)	false
CAL	CG2	THR- 99	4	0	Hydrophobic	false
CAT	CG2	THR- 99	3.87	0	Hydrophobic	false
CAR	CB	ALA- 142	4.21	0	Hydrophobic	false
OAE	OD1	ASN- 143	2.76	143.33	H-Bond (Ligand Donor)	false
CAT	CD2	LEU- 145	4.12	0	Hydrophobic	false
CBH	CD2	LEU- 145	4.35	0	Hydrophobic	false
CBD	CD2	LEU- 145	3.87	0	Hydrophobic	false
CBG	CD1	LEU- 145	3.78	0	Hydrophobic	false
CBM	CG2	VAL- 155	4.48	0	Hydrophobic	false
CAJ	CB	VAL- 155	4.07	0	Hydrophobic	false
CBI	CG2	VAL- 155	4.27	0	Hydrophobic	false
CAZ	CG1	VAL- 155	3.93	0	Hydrophobic	false
CBE	CG2	VAL- 155	3.98	0	Hydrophobic	false
CAI	CB	ASP- 156	3.85	0	Hydrophobic	false