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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:

2aot

1.900 Å

X-ray

2005-08-14

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Histamine N-methyltransferase
ID:HNMT_HUMAN
AC:P50135
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:2.1.1.8


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:36.779
Number of residues:25
Including
Standard Amino Acids: 24
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.1541404.000

% Hydrophobic% Polar
56.7343.27
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median2aotHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802040Highcharts.com
Ligand :
2aot_1 Structure
HET Code: 2PM
Formula: C17H22NO
Molecular weight: 256.363 g/mol
DrugBank ID: DB01075
Buried Surface Area:70.48 %
Polar Surface area: 13.67 Å2
Number of
H-Bond Acceptors: 1
H-Bond Donors: 1
Rings: 2
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 6

Mass center Coordinates

XYZ
52.947-12.712230.2645
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median2aotRingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation80510Highcharts.com


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
C3CD2LEU- 84.480Hydrophobic
C10CBTYR- 1463.570Hydrophobic
C14CH2TRP- 1793.60Hydrophobic
C7CZ2TRP- 1833.980Hydrophobic
C14CZ2TRP- 1834.10Hydrophobic
C10CBCYS- 1964.480Hydrophobic
C11SGCYS- 1963.750Hydrophobic
C12CE2TYR- 1983.470Hydrophobic
C14CE2PHE- 2434.380Hydrophobic
C2CE1PHE- 2433.470Hydrophobic
C4CBGLU- 2464.370Hydrophobic
N1OHOH- 6532.73157.37H-Bond
(Ligand Donor)