scPDB - 3t9i entry

Protein Data Bank Entry:

PDB ID : 3t9i

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2011-08-02

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:	41.054
Number of residues:	30
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.038	499.500

% Hydrophobic	% Polar
61.49	38.51
According to VolSite

Ligand :

HET Code:	3T9
Formula:	C19H15N3O2
Molecular weight:	317.341 g/mol
DrugBank ID:	-
Buried Surface Area:	73.2 %
Polar Surface area:	71.03 Å2

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

Mass center Coordinates

X	Y	Z
-22.0154	35.02	-0.748125

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
C19	CD1	LEU- 44	3.85	0	Hydrophobic	false
C14	CB	PHE- 49	4.37	0	Hydrophobic	false
C8	CG2	VAL- 52	4.3	0	Hydrophobic	false
C2	CB	ALA- 65	4.1	0	Hydrophobic	false
C16	CD	LYS- 67	3.59	0	Hydrophobic	false
C11	CD2	LEU- 93	4.44	0	Hydrophobic	false
C12	CD1	LEU- 93	4.46	0	Hydrophobic	false
C21	CD2	LEU- 93	3.55	0	Hydrophobic	false
C21	CG2	VAL- 103	4.39	0	Hydrophobic	false
C10	CG2	ILE- 104	4.36	0	Hydrophobic	false
C21	CB	ILE- 104	3.57	0	Hydrophobic	false
C11	CD2	LEU- 120	4.09	0	Hydrophobic	false
C21	CD2	LEU- 120	4.35	0	Hydrophobic	false
C9	CD1	LEU- 120	3.61	0	Hydrophobic	false
N5	O	GLU- 121	2.74	142.14	H-Bond (Ligand Donor)	false
C19	CD	ARG- 122	3.68	0	Hydrophobic	false
C23	CG1	VAL- 126	3.39	0	Hydrophobic	false
C2	CD1	LEU- 174	3.83	0	Hydrophobic	false
C13	CD1	LEU- 174	3.92	0	Hydrophobic	false
C14	CD1	ILE- 185	3.92	0	Hydrophobic	false
C10	CB	ILE- 185	3.65	0	Hydrophobic	false
C16	CB	ASP- 186	4.33	0	Hydrophobic	false
O18	N	PHE- 187	2.99	169.3	H-Bond (Protein Donor)	false
C21	CE1	PHE- 187	3.69	0	Hydrophobic	false