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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:

4l4v

1.900 Å

X-ray

2013-06-09

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Major histocompatibility complex class I-related gene protein
ID:HMR1_HUMAN
AC:Q95460
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A83 %
G10 %
H7 %


Ligand binding site composition:

B-Factor:18.536
Number of residues:32
Including
Standard Amino Acids: 30
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.376705.375

% Hydrophobic% Polar
47.3752.63
According to VolSite

Ligand :
4l4v_1 Structure
HET Code: 1VY
Formula: C12H16N4O7
Molecular weight: 328.278 g/mol
DrugBank ID: -
Buried Surface Area:78.46 %
Polar Surface area: 175.27 Å2
Number of
H-Bond Acceptors: 10
H-Bond Donors: 6
Rings: 2
Aromatic rings: 0
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 5

Mass center Coordinates

XYZ
-90.506765.480594.8767


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
C9CZTYR- 73.910Hydrophobic
C1'CD2TYR- 73.610Hydrophobic
O2NEARG- 92.8163.94H-Bond
(Protein Donor)
O3'NH2ARG- 93.03121.56H-Bond
(Protein Donor)
O4'NH2ARG- 92.87132.12H-Bond
(Protein Donor)
N3OGSER- 242.78164.79H-Bond
(Ligand Donor)
N5NZLYS- 433.1165.48H-Bond
(Protein Donor)
C9CE1TYR- 623.480Hydrophobic
C4'CZ2TRP- 694.20Hydrophobic
C3'CH2TRP- 693.790Hydrophobic
O3'NH1ARG- 942.84138.71H-Bond
(Protein Donor)
O2'OHTYR- 952.83161.74H-Bond
(Protein Donor)
C1'CG2ILE- 964.360Hydrophobic
C5'CD1ILE- 963.340Hydrophobic
O5'OHTYR- 1523.01154.04H-Bond
(Ligand Donor)
O5'NE2GLN- 1532.79171.66H-Bond
(Protein Donor)
C1'CZ2TRP- 1563.540Hydrophobic
O2OHOH- 4022.89179.97H-Bond
(Protein Donor)