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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:

2g6p

1.900 Å

X-ray

2006-02-24

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:22.576
Number of residues:21
Including
Standard Amino Acids: 21
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.974833.625

% Hydrophobic% Polar
42.5157.49
According to VolSite

Ligand :
2g6p_1 Structure
HET Code: HM2
Formula: C18H17ClN4
Molecular weight: 324.807 g/mol
DrugBank ID: DB07901
Buried Surface Area:49.05 %
Polar Surface area: 50.7 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 1
Rings: 3
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
20.596118.9214.651


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- 1924.240Hydrophobic
C3CBTYR- 1954.420Hydrophobic
C10CE2TYR- 1953.870Hydrophobic
C4CD2TYR- 1953.210Hydrophobic
C10CD1TYR- 1964.010Hydrophobic
C3CBPHE- 19840Hydrophobic
C2SGCYS- 2033.820Hydrophobic
DuArDuArHIS- 3103.40Aromatic Face/Face
DuArDuArHIS- 3103.40Aromatic Face/Face
CL1CBHIS- 3104.140Hydrophobic
C3CZ3TRP- 3533.480Hydrophobic
C14CZ3TRP- 3533.40Hydrophobic