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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:

1nce

2.400 Å

X-ray

2002-12-05

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Thymidylate synthase
ID:TYSY_ECOLI
AC:P0A884
Organism:Escherichia coli
Reign:Bacteria
TaxID:83333
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A97 %
B3 %


Ligand binding site composition:

B-Factor:37.086
Number of residues:40
Including
Standard Amino Acids: 37
Non Standard Amino Acids: 1
Water Molecules: 2
Cofactors: UMP
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.850671.625

% Hydrophobic% Polar
46.7353.27
According to VolSite

Ligand :
1nce_1 Structure
HET Code: CB3
Formula: C24H21N5O6
Molecular weight: 475.453 g/mol
DrugBank ID: DB03541
Buried Surface Area:60.35 %
Polar Surface area: 180.08 Å2
Number of
H-Bond Acceptors: 10
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 10

Mass center Coordinates

XYZ
14.519214.431634.6325


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
CP1CD1ILE- 794.050Hydrophobic
C12CG2ILE- 794.40Hydrophobic
C15CBILE- 793.560Hydrophobic
C9CZ2TRP- 803.940Hydrophobic
C8CZ2TRP- 833.330Hydrophobic
C8CD2LEU- 1433.640Hydrophobic
CBCE2PHE- 1764.320Hydrophobic
CP1CD1PHE- 1764.330Hydrophobic
CP3CBPHE- 1763.720Hydrophobic
NA2OALA- 2632.61122.03H-Bond
(Ligand Donor)
C7C5UMP- 5653.940Hydrophobic
O1OHOH- 5872.8129.88H-Bond
(Protein Donor)
OE2OHOH- 6512.82179.99H-Bond
(Protein Donor)