scPDB - 3bgp entry

Protein Data Bank Entry:

PDB ID : 3bgp

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2007-11-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	6.300	6.670	6.670	0.370	7.040	2

List of CHEMBLId :

CHEMBL409038

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:	65.543
Number of residues:	28
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.944	543.375

% Hydrophobic	% Polar
61.49	38.51
According to VolSite

Ligand :

HET Code:	VX1
Formula:	C17H11ClN4O
Molecular weight:	322.748 g/mol
DrugBank ID:	DB08707
Buried Surface Area:	54.67 %
Polar Surface area:	77.83 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	1
Rings:	4
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
22.2977	35.5381	-1.47683

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
C15	CD1	LEU- 44	4.37	0	Hydrophobic	false
N3	NZ	LYS- 67	2.89	165.08	H-Bond (Protein Donor)	false
C5	CD1	LEU- 120	3.39	0	Hydrophobic	false
C21	CG1	VAL- 126	4.42	0	Hydrophobic	false
C5	CB	ILE- 185	3.78	0	Hydrophobic	false