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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:

2ahr

2.150 Å

X-ray

2005-07-28

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Pyrroline-5-carboxylate reductase
ID:Q9A1S9_STRP1
AC:Q9A1S9
Organism:Streptococcus pyogenes serotype M1
Reign:Bacteria
TaxID:301447
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A2 %
B17 %
C80 %


Ligand binding site composition:

B-Factor:54.557
Number of residues:49
Including
Standard Amino Acids: 46
Non Standard Amino Acids: 0
Water Molecules: 3
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.312789.750

% Hydrophobic% Polar
50.8549.15
According to VolSite

Ligand :
2ahr_3 Structure
HET Code: NAP
Formula: C21H25N7O17P3
Molecular weight: 740.381 g/mol
DrugBank ID: DB03461
Buried Surface Area:55.89 %
Polar Surface area: 405.54 Å2
Number of
H-Bond Acceptors: 21
H-Bond Donors: 5
Rings: 5
Aromatic rings: 3
Anionic atoms: 4
Cationic atoms: 1
Rule of Five Violation: 2
Rotatable Bonds: 13

Mass center Coordinates

XYZ
53.8084101.10218.524


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
O2ANLYS- 103.04173.59H-Bond
(Protein Donor)
O2NNMET- 112.75161.04H-Bond
(Protein Donor)
C5DCBMET- 114.080Hydrophobic
C4NSDMET- 113.340Hydrophobic
C2BCBSER- 314.210Hydrophobic
O1XNEARG- 352.8162.61H-Bond
(Protein Donor)
O3XNH2ARG- 352.97163.15H-Bond
(Protein Donor)
O1XCZARG- 353.680Ionic
(Protein Cationic)
O3XCZARG- 353.750Ionic
(Protein Cationic)
N1ANE2HIS- 513.29156.11H-Bond
(Protein Donor)
O3DOILE- 652.94163.77H-Bond
(Ligand Donor)
C5DSDMET- 864.490Hydrophobic
C4DCGMET- 863.830Hydrophobic
O2DNALA- 883.09160.98H-Bond
(Protein Donor)
C5NSDMET- 1093.660Hydrophobic
C5NCGPRO- 1104.480Hydrophobic
O1NOGSER- 2212.69154.14H-Bond
(Protein Donor)
O2NOHOH- 15252.6153.63H-Bond
(Protein Donor)
O7NOHOH- 15993.17179.96H-Bond
(Protein Donor)