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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:

2uuk

1.390 Å

X-ray

2007-03-03

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Prothrombin
ID:THRB_HUMAN
AC:P00734
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:3.4.21.5


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:17.281
Number of residues:33
Including
Standard Amino Acids: 32
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.755567.000

% Hydrophobic% Polar
44.6455.36
According to VolSite

Ligand :
2uuk_1 Structure
HET Code: 897
Formula: C26H39N4O3
Molecular weight: 455.613 g/mol
DrugBank ID: -
Buried Surface Area:51.39 %
Polar Surface area: 84.81 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 3
Rings: 2
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 11

Mass center Coordinates

XYZ
4.0496718.568147.4677


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
C20CBHIS- 573.870Hydrophobic
C20CZ3TRP- 603.650Hydrophobic
C20CD2TYR- 603.670Hydrophobic
C24CE1TYR- 604.450Hydrophobic
C23CGLEU- 994.470Hydrophobic
C24CD2LEU- 993.710Hydrophobic
C19CD1LEU- 993.850Hydrophobic
C23CG2ILE- 1744.190Hydrophobic
N4OD2ASP- 1892.84165.87H-Bond
(Ligand Donor)
C13CBALA- 1904.350Hydrophobic
C13CG1VAL- 2133.680Hydrophobic
N3OSER- 2142.88172.15H-Bond
(Ligand Donor)
C23CD2TRP- 2153.630Hydrophobic
C16CBTRP- 2153.670Hydrophobic
O3NGLY- 2163.24155.33H-Bond
(Protein Donor)