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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:

1mu8

2.000 Å

X-ray

2002-09-23

Activity from ChEMBL: What is pChEMBL ?
MinMeanMedianStandard DeviationMaxCount
pChEMBL:9.0009.0009.0000.0009.0001

List of CHEMBLId :

CHEMBL143824


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:24.577
Number of residues:34
Including
Standard Amino Acids: 34
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.255421.875

% Hydrophobic% Polar
38.4061.60
According to VolSite

Ligand :
1mu8_1 Structure
HET Code: CDB
Formula: C21H21F3N6O2
Molecular weight: 446.426 g/mol
DrugBank ID: DB07549
Buried Surface Area:61.47 %
Polar Surface area: 99.57 Å2
Number of
H-Bond Acceptors: 6
H-Bond Donors: 2
Rings: 3
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 8

Mass center Coordinates

XYZ
16.9586-13.783823.26


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
C29CBHIS- 574.240Hydrophobic
C29CZTYR- 604.060Hydrophobic
C29CZ3TRP- 603.960Hydrophobic
C29CD1LEU- 994.090Hydrophobic
C33CD1LEU- 994.170Hydrophobic
C4CGLEU- 993.660Hydrophobic
C3CG1ILE- 1744.40Hydrophobic
F13CG1ILE- 1744.190Hydrophobic
F1CD1ILE- 1743.90Hydrophobic
C1CBALA- 1904.010Hydrophobic
C44CBALA- 1903.980Hydrophobic
F47CBVAL- 2134.420Hydrophobic
C1CG1VAL- 2133.820Hydrophobic
N37OSER- 2143.29154.07H-Bond
(Ligand Donor)
C3CBTRP- 2154.330Hydrophobic
C33CBTRP- 2153.980Hydrophobic
F13CE3TRP- 2153.360Hydrophobic
N18OGLY- 2163.19174.37H-Bond
(Ligand Donor)
O28NGLY- 2163.12163.75H-Bond
(Protein Donor)
F13CGGLU- 2173.380Hydrophobic