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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:

3rbq

2.000 Å

X-ray

2011-03-29

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Protein unc-119 homolog A
ID:U119A_HUMAN
AC:Q13432
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
D100 %


Ligand binding site composition:

B-Factor:21.919
Number of residues:45
Including
Standard Amino Acids: 44
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.314462.375

% Hydrophobic% Polar
55.4744.53
According to VolSite

Ligand :
3rbq_3 Structure
HET Code: GLY_ALA_GLY_ALA_DAO
Formula: C10H19N4O4
Molecular weight: 259.282 g/mol
DrugBank ID: -
Buried Surface Area:64.24 %
Polar Surface area: 132.01 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 4
Rings: 0
Aromatic rings: 0
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 7

Mass center Coordinates

XYZ
44.9099-22.21919.1089


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
CBCGPHE- 884.120Hydrophobic
CBCD1PHE- 913.720Hydrophobic
CBCBVAL- 1294.030Hydrophobic
CBCG2VAL- 14740Hydrophobic
NOE2GLU- 1632.96167.49H-Bond
(Ligand Donor)
NOGSER- 2182.93120.75H-Bond
(Ligand Donor)
OND2ASN- 2302.96142.67H-Bond
(Protein Donor)
NOHOH- 2522.91156.15H-Bond
(Ligand Donor)