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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:

4ikr

1.780 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:18.984
Number of residues:23
Including
Standard Amino Acids: 23
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.488344.250

% Hydrophobic% Polar
51.9648.04
According to VolSite

Ligand :
4ikr_1 Structure
HET Code: PVP
Formula: C16H21ClN5O
Molecular weight: 334.824 g/mol
DrugBank ID: -
Buried Surface Area:44.07 %
Polar Surface area: 66.58 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 2
Rings: 3
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
-2.29361-6.8246115.792


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
C2CBPRO- 1924.050Hydrophobic
C13CE2TYR- 1953.840Hydrophobic
C10CZTYR- 1954.440Hydrophobic
C13CD1TYR- 1964.180Hydrophobic
C3CBPHE- 1983.850Hydrophobic
C2SGCYS- 2033.80Hydrophobic
C10CBHIS- 3103.880Hydrophobic
CLCBHIS- 3104.260Hydrophobic
DuArDuArHIS- 3103.440Aromatic Face/Face
DuArDuArHIS- 3103.440Aromatic Face/Face
C4CZ3TRP- 3533.320Hydrophobic