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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:

3ada

2.200 Å

X-ray

2010-01-15

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Subunit alpha of sarocosine oxidase
ID:Q50LF0_9CORY
AC:Q50LF0
Organism:Corynebacterium sp. U-96
Reign:Bacteria
TaxID:31944
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:23.701
Number of residues:56
Including
Standard Amino Acids: 51
Non Standard Amino Acids: 0
Water Molecules: 5
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.284928.125

% Hydrophobic% Polar
52.3647.64
According to VolSite

Ligand :
3ada_1 Structure
HET Code: NAD
Formula: C21H26N7O14P2
Molecular weight: 662.417 g/mol
DrugBank ID: -
Buried Surface Area:70.1 %
Polar Surface area: 343.54 Å2
Number of
H-Bond Acceptors: 18
H-Bond Donors: 6
Rings: 5
Aromatic rings: 3
Anionic atoms: 2
Cationic atoms: 1
Rule of Five Violation: 3
Rotatable Bonds: 11

Mass center Coordinates

XYZ
-31.7467115.58322.2134


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
C3DCGPRO- 1373.880Hydrophobic
C4DCGPRO- 1373.890Hydrophobic
O2NNALA- 1382.98157.79H-Bond
(Protein Donor)
O3BOD2ASP- 1573.48122.88H-Bond
(Ligand Donor)
O3BOD1ASP- 1572.7168.93H-Bond
(Ligand Donor)
O2BOE2GLU- 1582.62167.54H-Bond
(Ligand Donor)
N3ANGLU- 1583.15142.67H-Bond
(Protein Donor)
C1BCGGLU- 1584.20Hydrophobic
O2BNEARG- 1592.94159.26H-Bond
(Protein Donor)
O1ANTHR- 1652.85166.61H-Bond
(Protein Donor)
O1AOG1THR- 1653.16143.1H-Bond
(Protein Donor)
O2AOG1THR- 1653148.12H-Bond
(Protein Donor)
C4DCBTHR- 1653.870Hydrophobic
N6AOVAL- 2042.79154.72H-Bond
(Ligand Donor)
N1ANVAL- 2043.14149.68H-Bond
(Protein Donor)
O1NNALA- 4172.81137.94H-Bond
(Protein Donor)
C5DCBALA- 4173.980Hydrophobic
C5NCBALA- 4174.390Hydrophobic
C5NCD2LEU- 4224.150Hydrophobic
C4NCBLEU- 4223.880Hydrophobic
C3DCBTHR- 4244.390Hydrophobic
O3DOG1THR- 4242.72172.48H-Bond
(Ligand Donor)
O2DOG1THR- 4243.32169.03H-Bond
(Ligand Donor)
C3DCBALA- 4274.50Hydrophobic
O1NOHOH- 9702.69179.94H-Bond
(Protein Donor)
O2NOHOH- 9782.62179.96H-Bond
(Protein Donor)