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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:

1xm1

2.300 Å

X-ray

2004-10-01

Activity from ChEMBL: What is pChEMBL ?
MinMeanMedianStandard DeviationMaxCount
pChEMBL:8.5208.5208.5200.0008.5201

List of CHEMBLId :

CHEMBL2368546


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:27.733
Number of residues:38
Including
Standard Amino Acids: 38
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.489739.125

% Hydrophobic% Polar
38.3661.64
According to VolSite

Ligand :
1xm1_1 Structure
HET Code: GAH
Formula: C38H63N11O6
Molecular weight: 769.977 g/mol
DrugBank ID: DB04697
Buried Surface Area:50.26 %
Polar Surface area: 298.2 Å2
Number of
H-Bond Acceptors: 10
H-Bond Donors: 11
Rings: 4
Aromatic rings: 1
Anionic atoms: 0
Cationic atoms: 2
Rule of Five Violation: 3
Rotatable Bonds: 21

Mass center Coordinates

XYZ
12.837-14.794614.0839


Binding mode :
What is Poseview ?
  • 2D View
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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
C27CBHIS- 574.340Hydrophobic
C27CZTYR- 604.350Hydrophobic
C27CH2TRP- 6040Hydrophobic
C51CH2TRP- 603.640Hydrophobic
C20CBASN- 984.370Hydrophobic
C19CD2LEU- 994.320Hydrophobic
C27CD2LEU- 993.620Hydrophobic
C20CD1LEU- 994.230Hydrophobic
C22CD1ILE- 1744.480Hydrophobic
C20CD1ILE- 1744.120Hydrophobic
C18CD1ILE- 1743.550Hydrophobic
O40OD1ASP- 1893.36171.32H-Bond
(Ligand Donor)
C38CBALA- 1903.650Hydrophobic
C49CGGLU- 1924.470Hydrophobic
C33CBSER- 1953.380Hydrophobic
C34CG1VAL- 2133.770Hydrophobic
C35CG1VAL- 2133.30Hydrophobic
N31OSER- 2143.36143.84H-Bond
(Ligand Donor)
C19CD2TRP- 2153.620Hydrophobic
C16CE3TRP- 2153.620Hydrophobic
O24NGLY- 2163.39172.79H-Bond
(Protein Donor)
C1CBGLU- 2173.850Hydrophobic
O46NGLY- 2192.76157.08H-Bond
(Protein Donor)
N47OGLY- 2192.95126.73H-Bond
(Ligand Donor)