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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:

1gjv

2.700 Å

X-ray

2001-08-03

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial
ID:BCKD_RAT
AC:Q00972
Organism:Rattus norvegicus
Reign:Eukaryota
TaxID:10116
EC Number:2.7.11.4


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:49.405
Number of residues:40
Including
Standard Amino Acids: 38
Non Standard Amino Acids: 2
Water Molecules: 0
Cofactors:
Metals: MG K

Cavity properties

LigandabilityVolume (Å3)
0.902904.500

% Hydrophobic% Polar
45.1554.85
According to VolSite

Ligand :
1gjv_1 Structure
HET Code: AGS
Formula: C10H14N5O12P3S
Molecular weight: 521.231 g/mol
DrugBank ID: DB02930
Buried Surface Area:67.8 %
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
96.6819119.81732.104


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
O1AND2ASN- 2493.1127.64H-Bond
(Protein Donor)
N6OD1ASP- 2852.91158.21H-Bond
(Ligand Donor)
C5'CBVAL- 2984.280Hydrophobic
C4'CG1VAL- 2983.850Hydrophobic
C1'CG1VAL- 2983.780Hydrophobic
C4'CD2PHE- 3034.250Hydrophobic
O1BOG1THR- 3042.63169.87H-Bond
(Protein Donor)
O3'NTHR- 3052.95167.03H-Bond
(Protein Donor)
O2'OG1THR- 3052.53159.28H-Bond
(Protein Donor)
C2'CG2THR- 3054.390Hydrophobic
O3BNGLY- 3373.13145.64H-Bond
(Protein Donor)
O2GNGLY- 3393.13139.95H-Bond
(Protein Donor)
O1ANLEU- 3403.4126.74H-Bond
(Protein Donor)
O2ANLEU- 3403.01167.71H-Bond
(Protein Donor)
C5'CD1LEU- 3404.040Hydrophobic
O2GMG MG- 13792.370Metal Acceptor
O2BMG MG- 13792.380Metal Acceptor
O1AMG MG- 13792.340Metal Acceptor