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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:

4jdc

1.600 Å

X-ray

2013-02-24

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Probable pyrroline-5-carboxylate dehydrogenase RocA
ID:O50443_MYCTU
AC:O50443
Organism:Mycobacterium tuberculosis
Reign:Bacteria
TaxID:83332
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:27.933
Number of residues:35
Including
Standard Amino Acids: 33
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.765880.875

% Hydrophobic% Polar
50.9649.04
According to VolSite

Ligand :
4jdc_1 Structure
HET Code: NAD
Formula: C21H26N7O14P2
Molecular weight: 662.417 g/mol
DrugBank ID: -
Buried Surface Area:61.69 %
Polar Surface area: 343.54 Å2
Number of
H-Bond Acceptors: 18
H-Bond Donors: 6
Rings: 5
Aromatic rings: 3
Anionic atoms: 2
Cationic atoms: 1
Rule of Five Violation: 3
Rotatable Bonds: 11

Mass center Coordinates

XYZ
47.49923.712728.8784


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
C1BCG2ILE- 1863.680Hydrophobic
C4BCG2ILE- 1863.590Hydrophobic
O3BOTHR- 1872.7163.76H-Bond
(Ligand Donor)
C5BCBPRO- 1884.370Hydrophobic
O2NNPHE- 1893.06152.71H-Bond
(Protein Donor)
O2BNZLYS- 2122.82156.43H-Bond
(Protein Donor)
C3BCBSER- 2144.150Hydrophobic
C5BCE1PHE- 2634.320Hydrophobic
O1AOGSER- 2663.01146.79H-Bond
(Protein Donor)
O1ANSER- 2662.81175.12H-Bond
(Protein Donor)
O1AOG1THR- 2693.2149.03H-Bond
(Protein Donor)
O1NOHCME- 3273.16166.48H-Bond
(Protein Donor)