scPDB - 2xj1 entry

Protein Data Bank Entry:

PDB ID : 2xj1

Resolution :2.130 Å

Experimental Method : X-ray

Deposition Date : 2010-07-01

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 pim-1
ID:	PIM1_HUMAN
AC:	P11309
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:	47.817
Number of residues:	35
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.094	469.125

% Hydrophobic	% Polar
60.43	39.57
According to VolSite

Ligand :

HET Code:	XJ1
Formula:	C19H22N4O2
Molecular weight:	338.404 g/mol
DrugBank ID:	-
Buried Surface Area:	68.32 %
Polar Surface area:	105.58 Å2

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

Mass center Coordinates

X	Y	Z
-22.1053	-34.1042	-1.83532

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
C20	CD1	LEU- 44	3.8	0	Hydrophobic	false
C3	CZ	PHE- 49	3.66	0	Hydrophobic	false
C4	CE2	PHE- 49	3.36	0	Hydrophobic	false
C16	CG1	VAL- 52	4.17	0	Hydrophobic	false
C18	CB	ALA- 65	3.39	0	Hydrophobic	false
O25	NZ	LYS- 67	2.77	160.59	H-Bond (Protein Donor)	false
O25	NZ	LYS- 67	2.77	0	Ionic (Protein Cationic)	false
C18	CD1	ILE- 104	3.94	0	Hydrophobic	false
C18	CB	LEU- 120	4.44	0	Hydrophobic	false
C20	CG	ARG- 122	4.27	0	Hydrophobic	false
C19	CB	ARG- 122	4.08	0	Hydrophobic	false
N8	OD1	ASN- 172	3.09	141.86	H-Bond (Ligand Donor)	false
C20	CD1	LEU- 174	3.55	0	Hydrophobic	false
C16	CD1	ILE- 185	3.85	0	Hydrophobic	false
C7	CD1	ILE- 185	3.39	0	Hydrophobic	false
C17	CG2	ILE- 185	4	0	Hydrophobic	false
N8	OD2	ASP- 186	3.11	154.23	H-Bond (Ligand Donor)	false
N8	OD2	ASP- 186	3.11	0	Ionic (Ligand Cationic)	false
O24	N	ASP- 186	2.98	157.68	H-Bond (Protein Donor)	false
O24	O	HOH- 2008	2.91	179.96	H-Bond (Protein Donor)	false