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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:

4hxx

2.090 Å

X-ray

2012-11-12

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:40.586
Number of residues:32
Including
Standard Amino Acids: 32
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.539297.000

% Hydrophobic% Polar
55.6844.32
According to VolSite

Ligand :
4hxx_1 Structure
HET Code: 1AY
Formula: C28H30Cl2N5
Molecular weight: 507.477 g/mol
DrugBank ID: -
Buried Surface Area:42.4 %
Polar Surface area: 67.31 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 2
Rings: 4
Aromatic rings: 4
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 2
Rotatable Bonds: 11

Mass center Coordinates

XYZ
20.810419.337418.5115


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
C17CBGLU- 1283.80Hydrophobic
C32CGGLN- 1293.740Hydrophobic
C33CDLYS- 1323.740Hydrophobic
C32CBLYS- 1323.310Hydrophobic
CL8CBPRO- 19240Hydrophobic
C6CD2TYR- 1953.030Hydrophobic
CL8CD1PHE- 1983.380Hydrophobic
CL8SGCYS- 2033.940Hydrophobic
C12CBHIS- 3104.490Hydrophobic
DuArDuArHIS- 3103.40Aromatic Face/Face
DuArDuArHIS- 3103.40Aromatic Face/Face
CL8CZ3TRP- 3534.410Hydrophobic