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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:

1yw7

1.850 Å

X-ray

2005-02-17

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Methionine aminopeptidase 2
ID:MAP2_HUMAN
AC:P50579
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:19.517
Number of residues:30
Including
Standard Amino Acids: 27
Non Standard Amino Acids: 2
Water Molecules: 1
Cofactors:
Metals: MN MN

Cavity properties

LigandabilityVolume (Å3)
1.005438.750

% Hydrophobic% Polar
59.2340.77
According to VolSite

Ligand :
1yw7_1 Structure
HET Code: A41
Formula: C14H12NO4S
Molecular weight: 290.314 g/mol
DrugBank ID: DB07313
Buried Surface Area:64.42 %
Polar Surface area: 94.68 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 1
Rings: 2
Aromatic rings: 2
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
16.903629.625518.206


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
C1CBALA- 2304.010Hydrophobic
O18NE2HIS- 2312.9162.82H-Bond
(Protein Donor)
C1CD2LEU- 3283.610Hydrophobic
C13CG2ILE- 3383.770Hydrophobic
C16CG1ILE- 3384.020Hydrophobic
C12CBHIS- 3394.040Hydrophobic
C13CEMET- 3843.790Hydrophobic
C20CBALA- 4143.890Hydrophobic
C20CGTYR- 4443.850Hydrophobic
C2CD1LEU- 4473.70Hydrophobic
O19MN MN- 4812.350Metal Acceptor