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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:

4jaq

1.730 Å

X-ray

2013-02-19

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Alpha-pyrone synthesis polyketide synthase-like Pks11
ID:PKS11_MYCTU
AC:P9WPF3
Organism:Mycobacterium tuberculosis
Reign:Bacteria
TaxID:83332
EC Number:2.3.1


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:18.654
Number of residues:34
Including
Standard Amino Acids: 34
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.964921.375

% Hydrophobic% Polar
72.1627.84
According to VolSite

Ligand :
4jaq_1 Structure
HET Code: COA
Formula: C21H32N7O16P3S
Molecular weight: 763.502 g/mol
DrugBank ID: DB01992
Buried Surface Area:44.78 %
Polar Surface area: 426.11 Å2
Number of
H-Bond Acceptors: 21
H-Bond Donors: 6
Rings: 3
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 3
Rotatable Bonds: 18

Mass center Coordinates

XYZ
38.3821-23.462289.357


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
CCPCD2LEU- 414.020Hydrophobic
CCPCBALA- 443.950Hydrophobic
CEPCBALA- 444.460Hydrophobic
S1PCBCYS- 1384.350Hydrophobic
CDPCG1VAL- 1833.510Hydrophobic
CDPCD1LEU- 1874.250Hydrophobic
C6PCD1LEU- 1873.890Hydrophobic
S1PCEMET- 2283.680Hydrophobic
N6AOLEU- 2413120.95H-Bond
(Ligand Donor)
C6PCD2LEU- 2414.460Hydrophobic
C2PCD1LEU- 2454.10Hydrophobic
N4POGLY- 2793.12164.72H-Bond
(Ligand Donor)
CEPCGPRO- 2814.160Hydrophobic
O1ANZLYS- 2823.04130.26H-Bond
(Protein Donor)
O9PNLYS- 2823.24157.65H-Bond
(Protein Donor)
O1ANZLYS- 2823.040Ionic
(Protein Cationic)
O2ANZLYS- 2823.540Ionic
(Protein Cationic)
O4ANZLYS- 2823.690Ionic
(Protein Cationic)
CAPCBLYS- 2824.330Hydrophobic
C6PCG2VAL- 2834.050Hydrophobic
C2PCG2VAL- 2833.840Hydrophobic
S1PCGMET- 3393.570Hydrophobic