scPDB - 4a4o entry

Protein Data Bank Entry:

PDB ID : 4a4o

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2011-10-18

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 PLK1
ID:	PLK1_HUMAN
AC:	P53350
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.11.21

Chains:

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

Ligand binding site composition:

B-Factor:	47.537
Number of residues:	37
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.786	550.125

% Hydrophobic	% Polar
57.67	42.33
According to VolSite

Ligand :

HET Code:	664
Formula:	C24H27F3N7O2
Molecular weight:	502.512 g/mol
DrugBank ID:	-
Buried Surface Area:	66.17 %
Polar Surface area:	88.75 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	3
Rings:	5
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
10.4271	46.5194	9.64564

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
C8	CD1	LEU- 59	3.99	0	Hydrophobic	false
C9	CD2	LEU- 59	3.7	0	Hydrophobic	false
C36	CB	LEU- 59	4.12	0	Hydrophobic	false
C10	CB	LEU- 59	3.85	0	Hydrophobic	false
F23	CD2	LEU- 59	4.05	0	Hydrophobic	false
C31	CB	CYS- 67	4.22	0	Hydrophobic	false
C36	CB	CYS- 67	3.95	0	Hydrophobic	false
C5	CB	ALA- 80	3.77	0	Hydrophobic	false
O35	NZ	LYS- 82	2.9	164.8	H-Bond (Protein Donor)	false
C5	CD1	LEU- 130	4.32	0	Hydrophobic	false
F25	CD2	LEU- 132	4.05	0	Hydrophobic	false
N1	N	CYS- 133	2.94	161.31	H-Bond (Protein Donor)	false
N7	O	CYS- 133	2.85	148.69	H-Bond (Ligand Donor)	false
F24	CB	ARG- 134	4.49	0	Hydrophobic	false
F25	CB	ARG- 134	4.07	0	Hydrophobic	false
C9	CG	ARG- 136	4.16	0	Hydrophobic	false
C16	CB	ARG- 136	4.41	0	Hydrophobic	false
C11	CD	ARG- 136	3.52	0	Hydrophobic	false
C12	CB	ARG- 136	3.94	0	Hydrophobic	false
F24	CG	ARG- 136	3.47	0	Hydrophobic	false
C16	CB	SER- 137	3.58	0	Hydrophobic	false
N18	OE1	GLU- 140	3.64	0	Ionic (Ligand Cationic)	false
N18	OE2	GLU- 140	2.68	0	Ionic (Ligand Cationic)	false
N18	OE2	GLU- 140	2.68	163.47	H-Bond (Ligand Donor)	false
C16	CE2	PHE- 183	3.73	0	Hydrophobic	false
C36	CE2	PHE- 183	4.25	0	Hydrophobic	false