Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

4iku

1.300 Å

X-ray

2012-12-28

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Methionine aminopeptidase 1
ID:MAP11_HUMAN
AC:P53582
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:14.053
Number of residues:24
Including
Standard Amino Acids: 24
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.216327.375

% Hydrophobic% Polar
49.4850.52
According to VolSite

Ligand :
4iku_1 Structure
HET Code: SHX
Formula: C19H18ClN5O
Molecular weight: 367.832 g/mol
DrugBank ID: -
Buried Surface Area:49.08 %
Polar Surface area: 93.79 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 2
Rings: 3
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 6

Mass center Coordinates

XYZ
20.7607-6.5688515.2348


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
C2CBPRO- 1924.220Hydrophobic
C10CE2TYR- 1954.190Hydrophobic
C3CBPHE- 1984.020Hydrophobic
C2SGCYS- 2034.020Hydrophobic
C17CE1TYR- 3003.490Hydrophobic
DuArDuArHIS- 3103.380Aromatic Face/Face
DuArDuArHIS- 3103.380Aromatic Face/Face
CLCBHIS- 3104.140Hydrophobic
C3CZ3TRP- 3533.360Hydrophobic
C15CZ3TRP- 3533.410Hydrophobic