scPDB - 4bzo entry

Protein Data Bank Entry:

PDB ID : 4bzo

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2013-07-29

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:	23.998
Number of residues:	30
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.188	570.375

% Hydrophobic	% Polar
59.76	40.24
According to VolSite

Ligand :

HET Code:	676
Formula:	C22H23FN5O2
Molecular weight:	408.449 g/mol
DrugBank ID:	-
Buried Surface Area:	63.74 %
Polar Surface area:	103.66 Å2

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

Mass center Coordinates

X	Y	Z
22.799	-35.3311	2.63237

Binding mode :

What is Poseview ?

2D View
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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
C27	CD1	LEU- 44	4.34	0	Hydrophobic	false
C26	CD2	LEU- 44	3.95	0	Hydrophobic	false
C14	CD1	LEU- 44	4.11	0	Hydrophobic	false
F18	CD1	LEU- 44	3.6	0	Hydrophobic	false
C25	CB	LEU- 44	3.85	0	Hydrophobic	false
C11	CZ	PHE- 49	3.86	0	Hydrophobic	false
C6	CE1	PHE- 49	3.6	0	Hydrophobic	false
C6	CG2	VAL- 52	4.01	0	Hydrophobic	false
C12	CG1	VAL- 52	4.27	0	Hydrophobic	false
C12	CB	ALA- 65	3.77	0	Hydrophobic	false
O10	NZ	LYS- 67	2.77	148.97	H-Bond (Protein Donor)	false
C13	CD1	ILE- 104	4.21	0	Hydrophobic	false
C13	CD1	LEU- 120	4.03	0	Hydrophobic	false
F18	CG	ARG- 122	3.52	0	Hydrophobic	false
F18	CG1	VAL- 126	4.04	0	Hydrophobic	false
C27	CG1	VAL- 126	3.86	0	Hydrophobic	false
N30	OD2	ASP- 128	3.96	0	Ionic (Ligand Cationic)	false
F18	CD1	LEU- 174	4.38	0	Hydrophobic	false
C28	CD2	LEU- 174	3.92	0	Hydrophobic	false
C14	CD1	LEU- 174	3.93	0	Hydrophobic	false
C13	CG2	ILE- 185	4.24	0	Hydrophobic	false
C6	CD1	ILE- 185	4.33	0	Hydrophobic	false
N8	OD2	ASP- 186	2.92	128.94	H-Bond (Ligand Donor)	false
O10	O	HOH- 2024	2.96	158.58	H-Bond (Protein Donor)	false
N20	O	HOH- 2037	2.86	169.97	H-Bond (Ligand Donor)	false