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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:

3ort

1.900 Å

X-ray

2010-09-07

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Serine/threonine protein kinase
ID:A5TY84_MYCTA
AC:A5TY84
Organism:Mycobacterium tuberculosis
Reign:Bacteria
TaxID:419947
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:45.001
Number of residues:37
Including
Standard Amino Acids: 36
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.563783.000

% Hydrophobic% Polar
44.8355.17
According to VolSite

Ligand :
3ort_1 Structure
HET Code: AGS
Formula: C10H14N5O12P3S
Molecular weight: 521.231 g/mol
DrugBank ID: DB02930
Buried Surface Area:61.7 %
Polar Surface area: 329.24 Å2
Number of
H-Bond Acceptors: 17
H-Bond Donors: 5
Rings: 3
Aromatic rings: 2
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 8

Mass center Coordinates

XYZ
8.5936140.519111.0634


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
O2GNGLY- 213.02165.7H-Bond
(Protein Donor)
O1BNMET- 222.93157.99H-Bond
(Protein Donor)
O1BNSER- 232.99143.32H-Bond
(Protein Donor)
C1'CBVAL- 254.060Hydrophobic
C5'CG2VAL- 253.990Hydrophobic
O2BNZLYS- 403.35134.95H-Bond
(Protein Donor)
O1ANZLYS- 402.72134.67H-Bond
(Protein Donor)
O2BNZLYS- 403.350Ionic
(Protein Cationic)
O1ANZLYS- 402.720Ionic
(Protein Cationic)
N6OGLU- 932.8149.39H-Bond
(Ligand Donor)
N1NVAL- 953.11159.19H-Bond
(Protein Donor)
C2'CG2THR- 993.940Hydrophobic
O3GNZLYS- 1402.82160.53H-Bond
(Protein Donor)
O3GNZLYS- 1402.820Ionic
(Protein Cationic)
C3'CEMET- 1554.460Hydrophobic