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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:

1zrb

1.900 Å

X-ray

2005-05-19

Activity from ChEMBL: What is pChEMBL ?
MinMeanMedianStandard DeviationMaxCount
pChEMBL:8.3608.7408.7400.3809.1102

List of CHEMBLId :

CHEMBL190687


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
A100 %


Ligand binding site composition:

B-Factor:23.258
Number of residues:33
Including
Standard Amino Acids: 33
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.063475.875

% Hydrophobic% Polar
46.1053.90
According to VolSite

Ligand :
1zrb_1 Structure
HET Code: 062
Formula: C26H26ClN4O4
Molecular weight: 493.962 g/mol
DrugBank ID: -
Buried Surface Area:59.74 %
Polar Surface area: 122.74 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 3
Rings: 5
Aromatic rings: 3
Anionic atoms: 1
Cationic atoms: 2
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
16.8966-14.219922.1111


Binding mode :
What is Poseview ?
  • 2D View
  • 3D View
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
C26CZTYR- 603.810Hydrophobic
C25CH2TRP- 603.420Hydrophobic
C5CD2LEU- 994.240Hydrophobic
C26CD2LEU- 993.940Hydrophobic
CL1CBALA- 1903.840Hydrophobic
C42CBALA- 1903.750Hydrophobic
CL1CG1VAL- 2133.590Hydrophobic
C41CG1VAL- 2133.620Hydrophobic
N36OSER- 2143.05164.85H-Bond
(Ligand Donor)
C5CBTRP- 2153.70Hydrophobic
N54OGLY- 2162.98151.72H-Bond
(Ligand Donor)
O63NGLY- 2163.1166.03H-Bond
(Protein Donor)
C44SGCYS- 2204.350Hydrophobic
CL1CZTYR- 2284.030Hydrophobic