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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:

4k1b

2.080 Å

X-ray

2013-04-04

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:40.793
Number of residues:36
Including
Standard Amino Acids: 34
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.103705.375

% Hydrophobic% Polar
53.5946.41
According to VolSite

Ligand :
4k1b_1 Structure
HET Code: 1OC
Formula: C26H25F2N8O
Molecular weight: 503.526 g/mol
DrugBank ID: -
Buried Surface Area:53.34 %
Polar Surface area: 116.61 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 4
Rings: 6
Aromatic rings: 5
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 1
Rotatable Bonds: 6

Mass center Coordinates

XYZ
-41.6108-2.12851-1.03914


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
C3CD2LEU- 444.070Hydrophobic
C7CD1LEU- 444.020Hydrophobic
F38CD1LEU- 443.390Hydrophobic
C9CBALA- 654.090Hydrophobic
N22NZLYS- 672.89171.99H-Bond
(Protein Donor)
DuArNZLYS- 673.75125.1Pi/Cation
N12OGLU- 1212.67172.67H-Bond
(Ligand Donor)
F38CDARG- 1224.140Hydrophobic
F38CG1VAL- 1263.610Hydrophobic
N34OD2ASP- 1282.680Ionic
(Ligand Cationic)
C6CD2LEU- 1744.070Hydrophobic
C9CD1LEU- 1743.660Hydrophobic
C36CD1ILE- 1854.120Hydrophobic
F37CG1ILE- 1854.450Hydrophobic
N34OHOH- 5483.02162.62H-Bond
(Ligand Donor)