scPDB - 5ap7 entry

Protein Data Bank Entry:

PDB ID : 5ap7

Resolution :2.450 Å

Experimental Method : X-ray

Deposition Date : 2015-09-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Dual specificity protein kinase TTK
ID:	TTK_HUMAN
AC:	P33981
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.12.1

Chains:

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

Ligand binding site composition:

B-Factor:	64.159
Number of residues:	38
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.090	934.875

% Hydrophobic	% Polar
41.88	58.12
According to VolSite

Ligand :

HET Code:	SVE
Formula:	C35H40F3N8O3
Molecular weight:	677.739 g/mol
DrugBank ID:	-
Buried Surface Area:	47.77 %
Polar Surface area:	127.49 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	4
Rings:	6
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
0.150796	-12.405	-14.9316

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
F39	CB	ILE- 531	3.61	0	Hydrophobic	false
C19	CD1	ILE- 531	4.24	0	Hydrophobic	false
F38	CG2	ILE- 531	3.39	0	Hydrophobic	false
C47	CB	SER- 537	3.51	0	Hydrophobic	false
C13	CG1	VAL- 539	4.34	0	Hydrophobic	false
C1	CG1	VAL- 539	4.24	0	Hydrophobic	false
C47	CG2	VAL- 539	3.52	0	Hydrophobic	false
F38	CG	GLN- 541	4.33	0	Hydrophobic	false
C13	CB	ALA- 551	3.74	0	Hydrophobic	false
O10	NZ	LYS- 553	2.76	174.83	H-Bond (Protein Donor)	false
C47	CD	LYS- 553	3.81	0	Hydrophobic	false
DuAr	NZ	LYS- 553	3.93	9.02	Pi/Cation	false
C2	CD1	ILE- 586	3.54	0	Hydrophobic	false
C1	CE	MET- 602	3.35	0	Hydrophobic	false
F38	CE2	TRP- 604	3.48	0	Hydrophobic	false
F37	CZ2	TRP- 604	3.61	0	Hydrophobic	false
N18	O	GLY- 605	2.81	125.69	H-Bond (Ligand Donor)	false
N15	N	GLY- 605	3.04	165.43	H-Bond (Protein Donor)	false
C22	CG1	ILE- 607	4.48	0	Hydrophobic	false
C34	CD1	ILE- 607	3.93	0	Hydrophobic	false
C23	CB	ASP- 608	4.22	0	Hydrophobic	false
C34	CB	SER- 611	4.14	0	Hydrophobic	false
C24	CD1	LEU- 654	4.24	0	Hydrophobic	false
C13	CD2	LEU- 654	3.92	0	Hydrophobic	false
C1	CG2	ILE- 663	3.88	0	Hydrophobic	false
C48	CG2	ILE- 663	3.69	0	Hydrophobic	false
C42	CB	ASP- 664	4.43	0	Hydrophobic	false
C48	CB	ASP- 664	4.26	0	Hydrophobic	false