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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:

3a99

1.600 Å

X-ray

2009-10-22

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:22.095
Number of residues:35
Including
Standard Amino Acids: 31
Non Standard Amino Acids: 1
Water Molecules: 3
Cofactors:
Metals: MG

Cavity properties

LigandabilityVolume (Å3)
0.858772.875

% Hydrophobic% Polar
47.1652.84
According to VolSite

Ligand :
3a99_1 Structure
HET Code: ANP
Formula: C10H13N6O12P3
Molecular weight: 502.164 g/mol
DrugBank ID: -
Buried Surface Area:50.59 %
Polar Surface area: 322.68 Å2
Number of
H-Bond Acceptors: 16
H-Bond Donors: 4
Rings: 3
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 8

Mass center Coordinates

XYZ
-9.7397482.9295-1.84581


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
C1'CBLEU- 444.060Hydrophobic
C1'CG1VAL- 524.110Hydrophobic
C5'CG2VAL- 524.140Hydrophobic
O1ANZLYS- 672.79164.41H-Bond
(Protein Donor)
O1ANZLYS- 672.790Ionic
(Protein Cationic)
N6OGLU- 1212.74153.67H-Bond
(Ligand Donor)
C3'CD1ILE- 1854.160Hydrophobic
O1BOHOH- 3382.95179.98H-Bond
(Protein Donor)
O3GOHOH- 3432.57179.96H-Bond
(Protein Donor)
O1GMG MG- 4012.160Metal Acceptor
O2BMG MG- 4012.090Metal Acceptor
O2AMG MG- 4012.130Metal Acceptor