scPDB - 3dcv entry

Protein Data Bank Entry:

PDB ID : 3dcv

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2008-06-04

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:	37.392
Number of residues:	25
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.981	482.625

% Hydrophobic	% Polar
62.24	37.76
According to VolSite

Ligand :

HET Code:	55E
Formula:	C17H14N2O2
Molecular weight:	278.305 g/mol
DrugBank ID:	DB07151
Buried Surface Area:	63.31 %
Polar Surface area:	62.02 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	1
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
17.9758	36.2738	1.67214

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	3.72	0	Hydrophobic	false
C14	CZ	PHE- 49	3.12	0	Hydrophobic	false
C6	CG1	VAL- 52	4.22	0	Hydrophobic	false
C16	CB	ALA- 65	3.46	0	Hydrophobic	false
O3	NZ	LYS- 67	2.85	152.48	H-Bond (Protein Donor)	false
C16	CG2	ILE- 104	4.22	0	Hydrophobic	false
C15	CD1	LEU- 120	3.52	0	Hydrophobic	false
O18	O	GLU- 121	2.54	168.8	H-Bond (Ligand Donor)	false
C20	CG	ARG- 122	4.29	0	Hydrophobic	false
C20	CG1	VAL- 126	4.41	0	Hydrophobic	false
C11	CB	GLU- 171	4.08	0	Hydrophobic	false
C19	CD1	LEU- 174	3.58	0	Hydrophobic	false
C15	CG2	ILE- 185	4.37	0	Hydrophobic	false
C6	CD1	ILE- 185	3.94	0	Hydrophobic	false