scPDB - 5dgz entry

Protein Data Bank Entry:

PDB ID : 5dgz

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2015-08-29

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:	39.869
Number of residues:	26
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.048	543.375

% Hydrophobic	% Polar
58.39	41.61
According to VolSite

Ligand :

HET Code:	L20
Formula:	C24H24N5O
Molecular weight:	398.480 g/mol
DrugBank ID:	DB08073
Buried Surface Area:	63.27 %
Polar Surface area:	94.23 Å2

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

Mass center Coordinates

X	Y	Z
40.2381	-2.78563	-1.6904

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
C1	CD1	LEU- 44	3.77	0	Hydrophobic	false
C32	CB	LEU- 44	3.91	0	Hydrophobic	false
C25	CE2	PHE- 49	3.61	0	Hydrophobic	false
C34	CZ	PHE- 49	3.42	0	Hydrophobic	false
C10	CG1	VAL- 52	4.2	0	Hydrophobic	false
C12	CG2	VAL- 52	4.26	0	Hydrophobic	false
C33	CB	VAL- 52	4.03	0	Hydrophobic	false
C6	CB	ALA- 65	3.75	0	Hydrophobic	false
N14	NZ	LYS- 67	3.17	144.98	H-Bond (Protein Donor)	false
C7	CG1	ILE- 104	3.92	0	Hydrophobic	false
C7	CD1	LEU- 120	3.94	0	Hydrophobic	false
N4	O	GLU- 121	2.81	160.05	H-Bond (Ligand Donor)	false
N21	OE2	GLU- 171	3.13	147.81	H-Bond (Ligand Donor)	false
N21	OE2	GLU- 171	3.13	0	Ionic (Ligand Cationic)	false
C25	CG	GLU- 171	3.94	0	Hydrophobic	false
N21	OD1	ASN- 172	2.76	173.79	H-Bond (Ligand Donor)	false
C1	CD1	LEU- 174	4.11	0	Hydrophobic	false
C11	CD1	LEU- 174	3.82	0	Hydrophobic	false
C8	CB	ILE- 185	3.88	0	Hydrophobic	false
C18	CD1	ILE- 185	3.85	0	Hydrophobic	false
C7	CG2	ILE- 185	3.92	0	Hydrophobic	false
C36	CD1	ILE- 185	3.41	0	Hydrophobic	false
C9	CD1	ILE- 185	3.87	0	Hydrophobic	false
N21	OD2	ASP- 186	4	0	Ionic (Ligand Cationic)	false
C16	CB	ASP- 186	3.9	0	Hydrophobic	false