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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:

2wm3

1.850 Å

X-ray

2009-06-29

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:NmrA-like family domain-containing protein 1
ID:NMRL1_HUMAN
AC:Q9HBL8
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:13.329
Number of residues:22
Including
Standard Amino Acids: 20
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors: NAP
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.376300.375

% Hydrophobic% Polar
60.6739.33
According to VolSite

Ligand :
2wm3_1 Structure
HET Code: NFL
Formula: C13H8F3N2O2
Molecular weight: 281.210 g/mol
DrugBank ID: DB04552
Buried Surface Area:66.38 %
Polar Surface area: 65.05 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
71.681816.757686.5134


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
C15CH2TRP- 823.880Hydrophobic
F1CE2TRP- 823.230Hydrophobic
F2CZ3TRP- 823.270Hydrophobic
C10CZ2TRP- 823.210Hydrophobic
O7NE1TRP- 822.55164.43H-Bond
(Protein Donor)
C13CBHIS- 1623.870Hydrophobic
F2CD1LEU- 2574.120Hydrophobic
C14CD1LEU- 2574.030Hydrophobic
C12CD2LEU- 2573.90Hydrophobic
C12CEMET- 2604.470Hydrophobic
C4SDMET- 2603.450Hydrophobic