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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

3qf9

2.200 Å

X-ray

2011-01-21

Interactomes:
Molecular Function:
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
A100 %


Ligand binding site composition:

B-Factor:39.756
Number of residues:30
Including
Standard Amino Acids: 27
Non Standard Amino Acids: 0
Water Molecules: 3
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.557418.500

% Hydrophobic% Polar
67.7432.26
According to VolSite

Ligand :
3qf9_1 Structure
HET Code: NM8
Formula: C33H29F3N4O4S
Molecular weight: 634.668 g/mol
DrugBank ID: -
Buried Surface Area:56.46 %
Polar Surface area: 123.46 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 2
Rings: 6
Aromatic rings: 4
Anionic atoms: 1
Cationic atoms: 1
Rule of Five Violation: 1
Rotatable Bonds: 8

Mass center Coordinates

XYZ
-19.916937.8535-0.547577


Binding mode :
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Binding mode
BioSolveIT 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
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
CAFCD1LEU- 443.630Hydrophobic
CAECD1LEU- 443.750Hydrophobic
CACCBLEU- 444.140Hydrophobic
SAQCG2VAL- 524.050Hydrophobic
NAONZLYS- 673.04161.44H-Bond
(Protein Donor)
CAFCGARG- 1224.440Hydrophobic
CAACG1VAL- 1263.60Hydrophobic
CADCD2LEU- 1744.310Hydrophobic
CAECD1LEU- 1743.990Hydrophobic
SAQCD1ILE- 1853.940Hydrophobic
OARNASP- 1863.19149.06H-Bond
(Protein Donor)
OAROHOH- 3272.82167.45H-Bond
(Protein Donor)
NAZOHOH- 3903.27151.8H-Bond
(Ligand Donor)