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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:

2ag8

2.100 Å

X-ray

2005-07-26

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Pyrroline-5-carboxylate reductase
ID:Q9K1N1_NEIMB
AC:Q9K1N1
Organism:Neisseria meningitidis serogroup B
Reign:Bacteria
TaxID:122586
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:41.685
Number of residues:46
Including
Standard Amino Acids: 43
Non Standard Amino Acids: 0
Water Molecules: 3
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.311297.000

% Hydrophobic% Polar
54.5545.45
According to VolSite

Ligand :
2ag8_1 Structure
HET Code: NAP
Formula: C21H25N7O17P3
Molecular weight: 740.381 g/mol
DrugBank ID: DB03461
Buried Surface Area:55.56 %
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
17.390726.156415.7582


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
O2ANASN- 103.48144.05H-Bond
(Protein Donor)
O1NND2ASN- 103.47168.28H-Bond
(Protein Donor)
O2NNMET- 113.07171.24H-Bond
(Protein Donor)
C3NCGMET- 113.910Hydrophobic
O1XNZLYS- 363.880Ionic
(Protein Cationic)
C1BCG1VAL- 653.890Hydrophobic
C3BCELYS- 663.630Hydrophobic
C3DCBALA- 884.420Hydrophobic
O2DNALA- 892.87171.02H-Bond
(Protein Donor)
C3NCEMET- 1103.680Hydrophobic
C5NSDMET- 1103.50Hydrophobic
C5NCGPRO- 1113.560Hydrophobic
O2NOHOH- 3512.52161.44H-Bond
(Protein Donor)