scPDB - 4jbp entry

Protein Data Bank Entry:

PDB ID : 4jbp

Resolution :2.450 Å

Experimental Method : X-ray

Deposition Date : 2013-02-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Aurora kinase A
ID:	AURKA_HUMAN
AC:	O14965
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.11.1

Chains:

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

Ligand binding site composition:

B-Factor:	43.388
Number of residues:	43
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.194	1076.625

% Hydrophobic	% Polar
52.04	47.96
According to VolSite

Ligand :

HET Code:	YPH
Formula:	C34H37N6O4
Molecular weight:	593.695 g/mol
DrugBank ID:	-
Buried Surface Area:	59.23 %
Polar Surface area:	125.98 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	5
Rings:	6
Aromatic rings:	5
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
6.29457	29.7434	6.54993

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
O34	NH2	ARG- 137	3.16	144.53	H-Bond (Protein Donor)	false
C7	CB	LEU- 139	4.1	0	Hydrophobic	false
C5	CD1	LEU- 139	4.23	0	Hydrophobic	false
C6	CD2	LEU- 139	4.07	0	Hydrophobic	false
C31	CB	PHE- 144	3.8	0	Hydrophobic	false
C5	CG1	VAL- 147	4.42	0	Hydrophobic	false
C16	CG2	VAL- 147	3.45	0	Hydrophobic	false
C22	CD	LYS- 162	4.33	0	Hydrophobic	false
C20	CD	LYS- 162	4.17	0	Hydrophobic	false
O33	NZ	LYS- 162	2.8	157.26	H-Bond (Protein Donor)	false
C32	CD2	LEU- 164	3.41	0	Hydrophobic	false
C30	CD2	LEU- 169	3.24	0	Hydrophobic	false
C30	CG2	VAL- 174	3.91	0	Hydrophobic	false
C29	CB	GLN- 177	4.34	0	Hydrophobic	false
C28	CD1	LEU- 178	3.38	0	Hydrophobic	false
C32	CD1	LEU- 178	4.29	0	Hydrophobic	false
C29	CB	LEU- 178	3.72	0	Hydrophobic	false
N24	OE1	GLU- 181	3.42	124.93	H-Bond (Ligand Donor)	false
N24	OE2	GLU- 181	3.11	162.22	H-Bond (Ligand Donor)	false
N26	OE1	GLU- 181	2.67	140.54	H-Bond (Ligand Donor)	false
C20	CD1	LEU- 208	4.46	0	Hydrophobic	false
C16	CD1	LEU- 210	4.31	0	Hydrophobic	false
C19	CD1	LEU- 210	3.54	0	Hydrophobic	false
N12	N	ALA- 213	3.33	148.24	H-Bond (Protein Donor)	false
C39	CG	ARG- 220	4.39	0	Hydrophobic	false
C5	CD1	LEU- 263	3.66	0	Hydrophobic	false
C17	CD1	LEU- 263	4	0	Hydrophobic	false
C17	CB	ALA- 273	3.97	0	Hydrophobic	false
C20	CB	ASP- 274	4.33	0	Hydrophobic	false
C22	CB	ASP- 274	3.28	0	Hydrophobic	false