scPDB - 2yac entry

Protein Data Bank Entry:

PDB ID : 2yac

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2011-02-18

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:	34.861
Number of residues:	37
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.686	631.125

% Hydrophobic	% Polar
46.52	53.48
According to VolSite

Ligand :

HET Code:	937
Formula:	C24H28F3N8O3
Molecular weight:	533.526 g/mol
DrugBank ID:	-
Buried Surface Area:	64.75 %
Polar Surface area:	135.86 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	4
Rings:	5
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-43.7539	11.3278	9.52195

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
C17	CD1	LEU- 59	4.3	0	Hydrophobic	false
C30	CB	LEU- 59	4.34	0	Hydrophobic	false
C21	CB	LEU- 59	3.92	0	Hydrophobic	false
F25	CD2	LEU- 59	4.12	0	Hydrophobic	false
C30	SG	CYS- 67	3.82	0	Hydrophobic	false
C5	CB	ALA- 80	3.61	0	Hydrophobic	false
O16	NZ	LYS- 82	2.8	147.86	H-Bond (Protein Donor)	false
C8	CG1	VAL- 114	4.12	0	Hydrophobic	false
C8	CD1	LEU- 130	3.48	0	Hydrophobic	false
F26	CD1	LEU- 132	3.89	0	Hydrophobic	false
N1	N	CYS- 133	2.89	155.88	H-Bond (Protein Donor)	false
N14	O	CYS- 133	2.88	162.78	H-Bond (Ligand Donor)	false
F26	CB	ARG- 134	4.12	0	Hydrophobic	false
F27	CG	ARG- 136	3.52	0	Hydrophobic	false
C37	CB	ARG- 136	4.34	0	Hydrophobic	false
C19	CB	ARG- 136	3.97	0	Hydrophobic	false
C20	CG	ARG- 136	3.66	0	Hydrophobic	false
C37	CB	SER- 137	3.58	0	Hydrophobic	false
N35	OE2	GLU- 140	2.73	162.34	H-Bond (Ligand Donor)	false
N35	OE2	GLU- 140	2.73	0	Ionic (Ligand Cationic)	false
N35	OE1	GLU- 140	3.8	0	Ionic (Ligand Cationic)	false
C7	CZ	PHE- 183	4.2	0	Hydrophobic	false
C29	CE2	PHE- 183	3.94	0	Hydrophobic	false
C37	CE2	PHE- 183	3.84	0	Hydrophobic	false
N28	OD2	ASP- 194	2.88	129.58	H-Bond (Ligand Donor)	false