Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

3opm

2.720 Å

X-ray

2010-09-01

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Dipeptidyl peptidase 4
ID:DPP4_HUMAN
AC:P27487
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:27.128
Number of residues:35
Including
Standard Amino Acids: 33
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.000374.625

% Hydrophobic% Polar
30.6369.37
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median3opmHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802040Highcharts.com
Ligand :
3opm_1 Structure
HET Code: LUI
Formula: C22H26N3O3
Molecular weight: 380.460 g/mol
DrugBank ID: -
Buried Surface Area:58.39 %
Polar Surface area: 100.27 Å2
Number of
H-Bond Acceptors: 3
H-Bond Donors: 2
Rings: 3
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 7

Mass center Coordinates

XYZ
17.8757-33.896214.7462
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median3opmRingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation80510Highcharts.com


Binding mode :
What is Poseview ?
  • 2D View
  • 3D View
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
N27OHOH- 13.08132.45H-Bond
(Ligand Donor)
N18OE1GLU- 2052.71144.39H-Bond
(Ligand Donor)
N18OE1GLU- 2052.710Ionic
(Ligand Cationic)
N18OE2GLU- 2062.93155.64H-Bond
(Ligand Donor)
N18OE1GLU- 2063.36124.12H-Bond
(Ligand Donor)
N18OE2GLU- 2062.930Ionic
(Ligand Cationic)
N18OE1GLU- 2063.360Ionic
(Ligand Cationic)
C22CE1PHE- 3573.440Hydrophobic
C25CD1TYR- 5473.690Hydrophobic
C4CBSER- 6304.090Hydrophobic
C13CBSER- 6303.740Hydrophobic
C15CBTYR- 6313.980Hydrophobic
C14CG2VAL- 6564.370Hydrophobic
N18OHTYR- 6622.8135.3H-Bond
(Ligand Donor)
C13CZTYR- 6623.450Hydrophobic
C15CZTYR- 6663.50Hydrophobic
C13CG2VAL- 7113.940Hydrophobic