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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:

1xny

2.200 Å

X-ray

2004-10-05

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Propionyl-CoA carboxylase complex B subunit
ID:Q9X4K7_STRCH
AC:Q9X4K7
Organism:Streptomyces coelicolor
Reign:Bacteria
TaxID:1902
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A29 %
B71 %


Ligand binding site composition:

B-Factor:36.682
Number of residues:46
Including
Standard Amino Acids: 42
Non Standard Amino Acids: 1
Water Molecules: 3
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.326857.250

% Hydrophobic% Polar
44.4955.51
According to VolSite

Ligand :
1xny_3 Structure
HET Code: 191
Formula: C24H37N7O17P3S
Molecular weight: 820.574 g/mol
DrugBank ID: -
Buried Surface Area:47.51 %
Polar Surface area: 431.53 Å2
Number of
H-Bond Acceptors: 21
H-Bond Donors: 6
Rings: 3
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 1
Rule of Five Violation: 3
Rotatable Bonds: 21

Mass center Coordinates

XYZ
47.1712-112.727-123.115


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
O14ND2ASN- 802.89128.4H-Bond
(Protein Donor)
C16CD1PHE- 1094.260Hydrophobic
C3CBALA- 1443.570Hydrophobic
N6NE2GLN- 1473.37154.1H-Bond
(Protein Donor)
CCD2LEU- 1533.460Hydrophobic
CCD2TYR- 1563.730Hydrophobic
ONGLY- 1833.38126.73H-Bond
(Protein Donor)
C3CG1VAL- 4443.950Hydrophobic
C11CD1ILE- 4534.330Hydrophobic
C12CG2ILE- 4533.390Hydrophobic
O5CZARG- 4562.940Ionic
(Protein Cationic)
O6CZARG- 4563.530Ionic
(Protein Cationic)
O15OHOH- 98122.98179.99H-Bond
(Protein Donor)