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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:

3utu

1.550 Å

X-ray

2011-11-26

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
H100 %


Ligand binding site composition:

B-Factor:17.959
Number of residues:39
Including
Standard Amino Acids: 38
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.625361.125

% Hydrophobic% Polar
45.7954.21
According to VolSite

Ligand :
3utu_1 Structure
HET Code: 1TS
Formula: C32H35ClN7O6S
Molecular weight: 681.182 g/mol
DrugBank ID: -
Buried Surface Area:60.06 %
Polar Surface area: 217.68 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 5
Rings: 4
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 2
Rotatable Bonds: 13

Mass center Coordinates

XYZ
16.5199-14.781323.2347


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
C34CBHIS- 574.450Hydrophobic
C12CH2TRP- 604.340Hydrophobic
C34CZ3TRP- 604.30Hydrophobic
C1CH2TRP- 603.60Hydrophobic
C10CE1TYR- 604.290Hydrophobic
C1CZTYR- 603.520Hydrophobic
CLCBASN- 984.370Hydrophobic
C10CD1LEU- 993.680Hydrophobic
C5CD2LEU- 994.160Hydrophobic
C34CD2LEU- 993.80Hydrophobic
CLCG2ILE- 1744.050Hydrophobic
C3CD1ILE- 1744.30Hydrophobic
C27OD2ASP- 1893.710Ionic
(Ligand Cationic)
C27OD1ASP- 1893.80Ionic
(Ligand Cationic)
N29OD1ASP- 1893.03148.09H-Bond
(Ligand Donor)
N28OD2ASP- 1892.95160.63H-Bond
(Ligand Donor)
C25CBALA- 1904.240Hydrophobic
C26CG1VAL- 2133.810Hydrophobic
N19OSER- 2143.01170.25H-Bond
(Ligand Donor)
CLCD2TRP- 2153.410Hydrophobic
C3CBTRP- 2154.460Hydrophobic
N11OGLY- 2163.11123.04H-Bond
(Ligand Donor)
O14NGLY- 2163.23166.55H-Bond
(Protein Donor)
C8CBGLU- 2173.580Hydrophobic
N28OGLY- 2192.8129.08H-Bond
(Ligand Donor)
C23SGCYS- 2204.470Hydrophobic